I think your question embedded two questions and should be dealt separately to give clear answer: a) How do Mahayana Buddhists make sense of prophecy of Maitreya? b) How do Vajrayana Buddhists make sense of prophecy of Maitreya when there are
son masters claimed to have achieved anuttara samyak sambodhi?
a) How do Mahayana Buddhists make sense of prophecy of Maitreya?
The answer for a) is very simple, almost needn't answer; Maitreya is the only next Buddha to come, it will take long long long time, 5.6 billion years according to one saying.
(i) Mahayana Buddhists (Chinese tradition) held there is only one future Buddha to come after Shakyamuni, that is, Maitreya. Though Mahayana has Sutra recounting the total of these 1000 Buddhas in this Noble Kalpa. All those enlightened, highest accomplished Bhiksus, Buddhists, even exhibiting supernormal abilities, are just achieving the Bodhisattva Bhumis accordingly. One Bhiksu achieved Bhumi level 8th, well-known said to be Ch'an Master Puan (1115-1169CE). There's no English info yet for him, English info has very tiny of the Chinese tradition. He belonged to the Lin Ji Zong (Rinzai) lineage, the 13th. For achieving 8th Bhumi, that Bodhisattva has penetrated the mystery of Dharani therefore is able to cite his own Mantra. Traditionally monastery will chant this Mantra during month of cleansing, to drive away bugs and insects, called Puan Mantra. He also made it as the Guqin melody. There is another Bhiksu called Zhigong (418-514CE), also achieved very high Bhumi surpassing material constrains but it's almost a standard practice for this type that he acted like a mad monk to conceal his identity (a Bodhisattva with advance Bhumi) in order to not to cause disturbance to society; or like Monk Budai (ceased 917CE), all these superior Buddhists will not make claim to the ordinary people who they are, not to say claiming as a Buddha, that's the Chinese tradition.
(ii) To be a Samyaksambuddha
(achieved anuttara samyak sambodhi) one must receive mark (授記) from previous Samyaksambuddha. Then there will be many many lives spent as Bodhisattva. In Buddha Shakyamuni's case, he received the mark from Buddha Dīpankara. The Theravadin's interpretation of Samyaksambuddha is incorrect, at least I read from this forum. Their interpretation mixed it the same as a Pratyekabuddha. Saying it meant self-awaken is not correct, for Buddha always learns from previous Buddhas - so are we here learning as well, Buddha has teachers; also self-awaken is not a sufficient factor, he must be marked by the previous Sam. Buddha he will be another Sam. Buddha. This is another reason why Lotus Sutra must exist and completely making sense. On the contrary, those traditions missing this Sutra or the like is missing out very important teachings - traditions with incomplete teachings. Yet those who attack the Lotus Sutra, either they held hidden agenda, or needed illumination.
(iii) Due to the above understanding, anyone claimed to be a Buddha, a living Buddha, a reincarnation of a Buddha, a next Buddha, demonstrating supernormal abilities to elicit followers, a Maitreya herein, a Maitreya to be... etc. they are fraudulent. Yet there're not lack of examples throughout history.
b) How do Vajrayana Buddhists make sense of prophecy of Maitreya when there are
son masters claimed to have achieved anuttara samyak sambodhi?
This was my puzzle too, when I just began my learning. I would have to declare that since I'm not following the Vajrayana tradition although I appreciate certain teachings found values in them also many historical great masters held my respect to, my answer should be regarded solely as personal opinion, derived from materials I studied only.
(i) I would sum up your referring only to the Tibetan Buddhism of the Zhügu (Living-Buddha, Tulku, reincarnation of a master) tradition. While I think it's possible the Buddhas could manifest their Nirmānakāya(s), but too many of those claims how many of them are real?
(ii) For Tibetan Buddhism, the undeniable fact is, that their religion and politics interwoven, hence, social status needed to establish for politican-monk. Historically, there're major schisms between the traditional Bon and Buddhism, and their merging and interfering. Very little is talked about, that during Tang Dynasty, Princess Wénchéng (628?-640CE) was granted to King Songtsän Gampo of Tibet, she took with her Bhiksus and Daoists, and scrolls1 of both schools. One of the Buddha Shakyamuni statues in Tibet today is reputedly said to be bought by her there. Also marked beginning the flourishing of Tibetan Buddhism; though there were Bhiksus coming directly from India before or after. From what I studied, Maitreya Buddha is not often focused, while Padmasambhava (?700?CE) was worshiped and also regarded the founder of Tibetan Buddhism. Padmasambhava appeared appro. 100 years after Wencheng's time, teaching Tantra, during the reign of Trisong Detsen (742-797CE). All these... serve quite a sound background and motive for claiming of reincarnation/continuation of certain established power player.
(iii) From here on, the emphasis of achieving Buddha-hood differs. Tibetan emphasizes on achieving Buddha-hood in one life-time, or maximum 7 lives, by practicing Tantra Yoga, with cultivation of merits/ Bodhicitta (Bodhicitta has many meanings too, not just about cultivation of the heart). One of the key methods is by "yoga-ing" (synchronizing) with the Guru, or the Yidam, so that one could acquire the same attributes of the Guru/Yidam, or the Guru can transfer his own achievement directly to the student... I'm still puzzling about how to discern these teachings, though I glean many useful knowledge from them. Up to this moment, I found that many of the evolved teachings (purely my own opinion) can be traced back to the (Chinese Mahayana2) Sutras, yet it's evolved, see? Just like many ignorant critics criticizing the Brahma Net Sutra of promoting self-immolation advocating burning oneself's fingers, body etc... even in the Chinese Buddhist community, they thought this so-called burning is a burning by the fire! Yet the disconnected interpretation could result in evolved teaching.
As in this case, one put aside the Maitreya prophecy, instead acknowledged there the Zhugu/Living-Buddha.
1. Scrolls in Chinese would be needed to translate into Tibetan, I assumed, hence evolved teaching from disconnected interpretation during translation. Example, when studying the Madhyamaka, since most of the English translations are based on Tibetan version, or so-called Sanskrit version, many of the analogies were incomplete/nonsensical, almost illegible, indicated these not only the translators' problem, could also be in the source texts. Yet such problem doesn't exist in the Chinese version of Kumarajiva's. Hence, it's logical to infer that the Tibetan is translated from Chinese, or Sankrit translated from Chinese then to Tibetan. Anyhow, the surviving versions Chinese is the oldest.
2. The translation of Sutras from Sanskrit (it's a generalized term since the ancient Chinese regarded all those such as Prakrit, Siddham... etc in one major group, called 梵語/Brahma Language) to Chinese was the most professional and under strictest rules, with large league often composed by more than 3000 Bhiksus/intellectuals, leading by great translators, such as Kumarajiva, Xuanzhang, Paramārtha3... etc. Since the Chinese language has highly modular capacity many Buddhist etymologies were created, that not only authentically transmitted the meaning, also enriched the Chinese vocabulary. Famous examples like: Tathagata = 如來, 12 Nidanas = 12 因緣, Vijnana = 識, Citta = 心... etc.
3. There is misleading writing in Wikipedia on Mahāsāṃghika4 quoting Paramartha said about how the Mahayana Sutras came about, that is completely a fabrication hidden under unknown agenda. What Paramartha left are just Sutras/Sastras translated, there's no record of his direct own words, how possible that Wikipedia amateur author is able to quot something that doesn't exist? Nevertheless, there is huge effort behind certain entity to promote what so-called Early Buddhism and sticking on Mahayana many different hats.
4. General accepted account of the schism in the 2nd Buddhist Council was initiated by the Elders who wanted to add more rules to the Vinaya. The sect who were the majority kept the original Vinaya without altering it since the Buddha's passing away was Mahāsāṃghika, school carried Mahayana teachings.