I think at least some of the Mahayana writers were self conscious atheists.
This is from the Fudo-Myo Sutra and is one of my favorite quotes:
He is the markless Dharmakaya, identical with [all-encompassing] space
itself, thus he has no dwelling. His only dwelling is in the minds and
thoughts of living beings.
So even in a system of Bodhisattvas, there is a subset of people who are skeptical about all the supernatural and see the Bodhisattvas (and all the other being unsubstantiated by evidence) as role models, pedagogical tools, rhetorical devices and so on.
This does not change the fact that there is a huge group of lay followers and historical monastics who clearly took the celestial Buddhas, Pure Lands, the realms, a semi-sentient Karma and a permanent, rebirthing soul as literal truths and true on account of faith.
In Basic Teachings of the Buddha, by Glenn Wallis (his old work that predates his current project), the author at points argues that the historical Buddha was an atheist and a nihilist that had no choice but to speak in the theological terms of the culture around him.
My own analogy is this-- it's like if you wanted to explain how evolution worked to a theist Christian, but didn't really care if the audience was atheist or not. Such a hypothetical teacher might teach about evolution as designed by God. In the same way the historical Buddha used the language of Karma, Dharma, Rebirth, Brahma to discuss a program of morality, restraint as part of a program to end suffering.