Does will mark future reference?
Sometimes. Probably more often than not. But not always.
My real question is about whether will should be considered part of the tense system or modal system.
Yes. One or the other, and sometimes both.
I'm becoming skeptical to how helpful a possible oversimplification can be.
Skepsis is healthy. But oversimplification is not merely helpful, it is essential to learning, right up to the point where it isn't.
Students and teachers have to start somewhere, and that somewhere has to be at the front end, where the student is in a state of more or less complete simplicity; teachers cannot begin by assuming subtleties the students have not yet achieved. So teachers start with the simple and intuitive division of temporal reference into "past"–"present"–"future". They provide simple and easily grasped handles on the language like were–are–will be, which they call "tenses", because they have to call them something. And they carefully avoid defining their terms too narrowly, and carefully shield students from gnarly real-life situations where were marks present tense and will marks modality and are has to be replaced with be — until they're ready to teach those uses.
It's pretty harmless, as long as the teachers are at that point willing to acknowledge that most of what they've taught is "baby rules" (aliter a pack of lies) which have very little to do with English-as-she-is-actually-spoken, and as long as they have something better and subtler to teach when they reach that point. Granted, few are willing and few do have something better; but it doesn't matter all that much, because when the students reach that point they figure it out for themselves, just as you have done.
Moreover, the students are now beginning to learn EASIAS the way native speakers do: not from grammar books, and certainly not from teachers (who in at least in US high schools know much less about English grammar than, say, your average third-year EFL student), but from speaking and listening and reading and writing. With that, they can build their own grammars from inside the language.