Zen is definitely its own animal. Why the practices, monastic laws, daily schedules vary so vastly from even other East Asian instantiations of Buddhism could be a subject of a book of its own. You could pull another book just out of the differences between Chinese Chan and Japanese Zen. But to respond to some of your examples...
On the subject of late dharma talks... My guess is that Master Dogen's dharma talk was given during a sesshin or period of intensive meditation practice. During these retreats, which consist of about a week of 12+ hour a day sitting, one common practice is the all night vigil/sitting. Generally what happens is that the abbot will give a dharma talk and retire to bed while the rest of the sangha sits in meditation until they drop off asleep (there's more to this absolutely beautiful practice, but this will do for now). This happens at the end of the day (around 10:30PM in our sangha, but it just as well could be midnight). And trust me, no lamp oil was being burned. (Most Zen monasteries aren't even heated!) Dharma talks aren't prepared. They are almost always extemporaneous. Dogen wouldn't have been reading anything. That talk would mostly likely have been recorded after the fact.
Regarding the late day meal... This is what is called "medicine"...which the Buddha said could be taken at any time. That's probably a bending of the rules. Ok, that's definitely a bending of the rules. But keep in mind that Zen monks work. Most of their sustenance comes from monastery farms. They also do all the upkeep to their temples, cook, wash the floors, patch roofs, etc. Generally speaking, they simply require more calories than a mendicant who doesn't do those things.
Don't try to understand Zen in terms of Theravadan Buddhism. There's a lot that they have in common, but the two traditions are separated by a vast tract of land and at least 1300 years. There's bound to be irreconcilable differences.