Some things I'd love to concretely establish, and discuss:
I will try answer with some of my own views, but keep in mind they will be generalized and any specifics depend on the game itself. I may also try mixing in some other views that are not necessarily mine
A) At what point is a Pokemon considered ''overleveled'' compared to a boss (e.g. is fighting Bugsy's L16 Scyther with a L18 Pidgeotto overleveling)?
in BW1, we had a "two levels above the boss's ace" policy because it wasn't exactly too hard to match that level or even have a level above that. In games like USUM, Exp. Share keeps you a few levels above each boss (in most cases. Bosses like Nanu are only two levels below you in worst cases and Ultra Necrozma generally outlevels you). Personally, if you didn't go out of your way to overlevel, I think one-two levels is fine. It is also important to factor in the possibility of a viability-changing factor in some of those levels; for example, if being one level above the ace gives the Pokemon an important move or causes an evolution, I find it very reasonable to actually overlevel there, since that's what most people would do anyways.
e: just to make it clear, I am not advocating for overleveling against opponents like HGSS Lance which will be outleveling you, I think it is impossible to match his levels in HGSS, I am mostly referring to the fights that were designed properly.
B) Are there any times when overleveling can be justified (e.g. to evolve or learn a move that is 1-3 levels away)?
read the above
C) Is wild grinding totally off limits or are there times they can be justified (e.g. you obtained a new Pokemon in a game, but they're underleveled compared to your team and thus you want to bring them up to speed against Heracross, Audino, Chansey, etc...)
Grinding is generally to be avoided, but if you are transparent about it, I think you should be fine (e.g. "hey guys, I wanted to test this fifth Pokemon just to mark off all Pokemon in this area, but I had to grind it so it can catch up with my teammates". In this case, you make it clear that you grinded your Pokemon and we know if this distorted the performance in any ways). Note that grinding off exclusively Chansey or anything will result in you having EVs mostly in one stat, so that may distort the actual performance, at least partially, but this depends on the game
D) Are X Items fully disallowed (e.g. using, say, a Dire Hit for Razor Leaf in GSC, to give you 50% crit rate)?
Some lists discourage them, other ban them, each list has a way to deal with them that it thinks is the most appropriate. I think Roto Boosts and X Items should be banned in Alola (even though I technically didn't ban them, but I avoid banning stuff where possible), as +1 to all stats or +2 to any stat is certainly going to distort a large amount of Pokemon's performances. HOWEVER, I am fine with X Items (and Roto Boosts) against opponents like HGSS Lance or Ultra Necrozma, as your "natural" checks to them are at best handful only (UN without X Items / Roto Boosts is only beaten by gimmicks like Focus Sash Counter / Mirror Coat / Perish Song / Curse / etc.).
In general, though, I understand your view on X Items and wanting to ban them, I personally prefer not to use them either in most of my runs. I think there are cases where they can be justified, but mostly for insanely difficult opponents, rather than for completing the game as quickly as possible. This also comes a bit to my view as to what is "efficient". I see efficiency moreso as "get through the game with as little hassle as possible" rather than get through it as fast as possible (of course, hassle also includes slowness (I wouldn't want to spend 40 turns on a single battle), I just don't put as much emphasis on speed).
E) Are Eggs ever going to be considered (e.g. hatching a Chikorita that has Leech Seed)?
In line with my view on efficiency, eggs should definitely not be considered (at least seriously). They are a hassle to get and hatch (not to mention a time sink anyways). Furthermore, you need to keep in mind that if you hatch something late into the game, you will have to grind it. I also few like not a lot of people will go out of their way to hatch eggs just to make a Pokemon viable. So I think eggs shouldn't be considered, because they aren't efficient and aren't ultimately a good indicator of a Pokemon's performance, in my opinion.
Personally, I think matchups are the most important currency or at least should be
I agree with the general statement, but I believe that it is also important to consider how you reach that performance. If I have to hunt a 1% / 5% Pokemon with a specific ability to achieve its best performance, that should definitely knock it down in tiering. lIkewise, in RBY, if a Pokemon depends on a contested TM (like Psychic) to perform well, this should also be considered against it. Although, in the next games, I don't think TM dependancy is an exacti issue, as you generally have a good variety of Pokemon and therefore you can afford to have a team where only one Pokemon needs that TM, though if you do require multiple valuable TMs, that should still be taken into account.
(and I saw you talk about the TMs, I just wanted to add up some more details about it).
Availability comes last as rare Pokemon aren't necessarily ''too rare'' (even the swarm Pokemon can literally appear on your first try to look for them).
there's another issue with rare availability in that it's harder to find one with acceptable IVs and nature. If I get a 1% encounter Pokemon with terrible IVs, I either receive a reduced performance or I need to hunt again and the chances of me stumbling across it so soon again are not very high.
(if I didn't answer something, I agree with / have no stake on / lack the expertise to answer it, didn't see it, or any other reason)