Thunderous Cacophony said:
The old "All drow are Chaotic Good" problem.
Personally, I have no problem with humanoid races being totally evil, especially something like Kuo-Toa. They're a race of mad fish-monsters known for being religious zealots of dark gods and plotting their return to dominance, only interacting with surface folk when raiding seaside villages and ships. Their minds are so alien that I feel comfortable saying that they have no concept of Good that relates to Good as understood by the demi-humans.
As a DM I've always maintained a limit on PC's using a monster race that usually is of an evil type alignment to have a maximum alignment shift of True Neutral. And if the player sufficiently roleplays the leeward shift towards a Good alignment the maximum shift would be a neutral good, with a huge negative bias from all good aligned races, much like the way RA Salvatore writes the general world's reaction to the aberrant Drizzt Do'Urden.
By the negative bias and pressures of being persecuted for the PC's race's crimes keeps said PC from ever gaining any further shifts towards Good alignments. And as I said, they have to work very hard in roleplaying the alignment shift and said alignment shifts will have heavy negative penalties as outlined in most DM guides. I'm unaware of most of the post-4th edition rules so I go by the earlier additions for support on alignment shifts.
My house rule has always been if an alignment shifts from one column to the other (evil to neutral, neutral to good) then the player loses one level of said character and if they're a form of a cleric they lose all cleric attributes and become a basic fighter with no retroactive bonuses like hit points adjustments. Plus a normally religious follower losing his/her/its faith in a deity has extreme world shattering implications and it must show through with a PC by way of penalties and possible class shifts. Sure one could at some point find faith in another deity but said deity will be wary of granting boons to a PC that has abandoned one deity, no matter what alignment and said PC must go above and beyond to prove his/her/its faith. If the deity shift is a totally opposing shift, chaotic to lawful, good to evil, etc., then said new deity may require a large personal sacrifice that would cause the PC a lot of introspection and personal suffering to even consider. The initial hard part though would be to even find a way to get said deity's attention.
In regards to mechanics of a cleric changing faiths and what they'd keep as a non-cleric would be any skills related to religion and arcana that the character previously held. Knowledge isn't stripped, just the faith based mechanics that would suffer. The player also has a choice of class shifting or not, depending on what the character's perspective would allow.
The reasoning behind the True Neutral alignment is much akin to how you described the perception of evil demi-humans not having said perspective of the term "good" and "evil". True Neutral allows them to be skeptical of their own races habits and likewise more open minded to learn of other perceptions but wary of falling into a trap of tunnel-vision.
Alignment shifts have to be weighed carefully as a DM because simply allowing a player to declare an alignment shift with no negative connotations allows for examples like: A lawful good wizard changing his/her alignment to neutral evil in order to perform necromantic spells that involve sacrificing living things then switching back later so as to avoid going against their alignment and being unable morally to perform said spells.
I try not to be too rules-heavy in my games but I do want my players to understand their characters motivations and moral compasses before they take actions in the game. If something a player declares intent to act upon and said action does not match up with the character's alignment, I may mark it in a column and keep it on record and depending on further acts beyond the first, if they continue committing acts against the alignment, then said character may just have a total alignment shift and all the negative connotations that go with it. Paladins shifting from lawful good to even chaotic good would lose their status as a paladin, etc.
I've had a lot of experience in D&D alone, my other TTRPG experiences notwithstanding, and I have cultivated a basic 10 commandments style house rules list. Alignment and non-traditional races are two of those house rules, of which you've read a good piece of. If you want to know the rest I'll gladly lay them out for you.