any additions or changes should be in keeping with the tone, themes, character and feel of the setting.
I've never said otherwise. I think we're coming at it through from opposite ends.
I've never advocated that an element from the PHB shouldn't be adapted to the setting, I'm all for re-flavoring tieflings from "scions of Asmodeus" to "powerful beings who dealt with fiends of the Wastes". I'm not against Dark Sun have a specific "Athasian" subrace for dwarves, elves, and halflings and not allowing the PHB subraces). I'm also fine with minor edits AS LONG AS SOMETHING IS GIVEN IN RETURN (The eldritch knight is unavailable, but here is the new Gladiator subclass to replace it).
And yes, that means bending the setting some to fit the rules; Calibans are completely a way to replace half-orcs in Ravenloft; it had no basis in the lore of the setting in 2e, no hint such things existed prior. It serves a specific need; we took an option that would not fit well with the setting and reworked it so that it did. How easy would it have been to just say "no half-orcs in Ravenloft?" I lot less words than coming up with a replacement race, complete with culture and history.
And sometimes, rarely, it just doesn't fit. You can't play a Triton in Athas; no matter how much refluffing you do. Those should be the rare exceptions staked out ONLY when refluffing and reworking have no viable alternative.
If it were up to me and I had to set the rules for any 5e conversions, These would be my guiding principles.
1.) Find a way to incorporate every PHB race. If a race cannot be incorporated (gnomes in DS, half-orcs in RL) than a replacement race should be added (muls, calibans). Its fine to limit subraces (all halflings in DL must take the kender subrace).
2.) Fit all PHB classes into the setting. This will require judicious use of re-fluffing and new/changed subclasses to make work. Not every subrace need be allowed (and in fact, more than few might not be) but the idea is to design as few new classes as possible and remove as few options as possible. If there is absolutely no way to incorporate a class (paladin in DS) add a sidebar explaining and give DMs option if they want to add it back). That will mean a few options get redone in ways that might not sit initially well (Oath of Solomnia for paladins vs a proper knight class) and new options/tweaks for classes might need to go on (giving all arcane casters the option to defile).
3.) Try to use as much of the PHB/DMG/MM material as possible in regards to spells, magic items, monsters, etc. Liberal use of re-fluffing is acceptable here.
4.) Optional Books (Volo, SCAG, Xanthar) are not bound to the above design aesthetics; the default for such options in new settings is "off" unless the DM wants to include it. A few exceptions (artificer in Eberron, mystic in DS) where the option is assumed are spelled out clearly.
5.) The design goal is always "how does this option fit in a gothic-horror/post-apocalyptic/high-romance/sword-n-sorcery/non-western world?" Just because it wasn't allowed before doesn't mean it automatically shouldn't be allowed now. Guidelines for making it fit rather than prescriptions of what does/doesn't.
6.) Its still D&D. In a fight between the core principles of D&D and the implied flavor, D&D should get the nod. For example, there should be no outright banning of arcane or divine magic, no mono-racial/human only settings, no magic items, etc. You are changing the SETTING of a D&D game, not D&D itself. Its to change how D&D is played, not give them a new game using the D&D base mechanics.
7.) Try to limit new over-arching mechanics when possible. DM should not need to remember more than TWO new mechanical subsystems to run a setting on top of the Core D&D rules. When possible, use the DMG options and base rules instead of inventing/reinventing new ones (RL should use the DMG fear/horror/madness rules; DS the existing heat/survival rules). The more rules you pile on the setting, the harder it is for the DM.
8.) The ideal Setup: Core Books + Setting Book. A setting should be playable with the Core Rules plus a copy of the supplemental stuff. A Player should also still have some options if he doesn't own the setting book; it shouldn't be a barrier for entry to the world.
9.) Together, but not the Same. Each setting is part of the D&D Universe. That means more than just sharing mechanics, but sharing some assumptions. That doesn't mean each setting adheres slavishly to the lore, but the concept that Athas exists in the same multiverse as Kyrnn or Faerun should at least be left open.
10.) Keep power-levels consistent. Ideally, A PC from another world should be about as powerful as one from another world. Dark Sun PCs don't need to have natural ability score caps of 24, Dragonlance PCs shouldn't be limited to 18th level max. An Athasian fighter shouldn't overpower a fighter from Faerun or Ravenloft. A cleric in Ravenloft shouldn't have all his spells and powers nerfed by the Dark Powers either. Some limits of course are needed for flavor (some form of rule for Athasian non-metal gear; or Ravenloft banning planar travel to stop PCs from teleporting out at earliest convenience). The biggest goal would be that all options are equal to allow a DM to pick an option or character from Ravenloft or Dark Sun and use it in his homebrewed or Faerun game without worrying its too powerful/weak.
That's how I'd do it. My goal is for a setting to change the theme of the game, not the game itself. It should be accessible, require minimum fuss, and still "feel like D&D" when played.