@AxConsortium
Boy, am I glad to see this. Thank you! I really appreciate it. In fact, this was one of the reasons I haven't started any new playthroughs.
You were actually supposed to get my proposal as a private message, so I could share some insight on what could be affected by the mod. But you were my second choice, and it's been a while since my first choice was active, so I opted to wait till they responded, though it's been months.
I figured I'd dump all of it here, in case you find some of it useful for the purpose of fine-tuning. But I'm very glad with the mod as it is. I reference StrategyWiki to refer to the checks and dialogue trees. The only convos that matter for this mod are the two right below, but I also included everything affected by the reputation mechanic or the companion assignment, for reference.
Affected convos:
Docks convo after Landing Rights/Visquis's message
This is the interaction with Hanharr or Mira that you miss if you're using the Choose Mira or Hanharr mod and your alignment leads to the interaction with the one that you end up not choosing. With the reputation over alignment mod, the convos and results flow seamlessly—you get approached and warned by the bounty hunter that ends up joining you. Favor with the Exchange (>=2) gets you Hanharr, and mixed (<2, > -4) and disfavor (<= -4) gets you Mira. Since you get Mira as a gray Exile, you get her with mixed standing with the Exchange as well.
If Mira is the one to approach you, her second line varies, but StrategyWiki doesn't show whether the condition is alignment or Exchange standing. Since what the line references is your actions while on Nar Shaddaa, Exchange reputation should be the condition (negative for one, mixed for the other).
The ideal approach, however, given that one line specifically refers to saving everyone, could be to set killing Saquesh, the boss at the Refugee Quad, as the condition, as this results in freeing the refugees from Exchange oppression.
Docks convo with alignment check
This, however, is the point where supposedly the game assigns your crewmate, way before the other convo. This alignment check would remain as it is for the purpose of Mira's line, just without the assignment of your future companion based on alignment.
So for the reputation check, the logical route would be placing it after the moment the game checks whether you have enough reputation to continue (more info below), but before either Mira or Hanharr approaches you at the Docks.
Other convos of note:
Mandatory Docks convo with Mira
This interaction with Mira takes place regardless of your future crewmate.
Fight at the combat pit
This is the point in the game where the new companion becomes playable.
Darth Traya's forecast
The last section here shows Kreia's foretelling of each planet's future. In Nar Shaddaa's case, the condition seems to be the fate of the refugees, but I have no way to be sure.
Convos already making use of the reputation mechanic:
Exchange reputation choices – Visquis's message is covered there as well further below.
These are all the choices the player has to get the Exchange's attention and gain or lose their favor. Once you get at least 8, regardless of favor or disfavor, Visquis's message will trigger at the landing pad. You could be a LS Exile who assumes wrecking havoc will get them nowhere or just get everyone killed, and thus tries to get the Exchange's attention by gaining their favor; or you could be a DS Exile who simply seeks to wreck havoc. Regardless of their intentions, what the game should check is what actions the Exile made while on Nar Shaddaa, not how they are morally as a whole.
Rodent convo at the Entertainment Promenade
This is the mechanic the game allows for the player to check their standing with the Exchange. StrategyWiki seems to show the option with the highest favor is missing a response, though I haven't checked this. The reputation over alignment mod makes this mechanic more useful as well.
One-sided Docks convo with Zez-Kai Ell
This is the first interaction with Zez-Kai Ell, and one of the two times your standing with the Exchange is checked. This is also where the conditions are laid down:
+2 or more for favor
less than +2 and more than -4 for mixed
-4 or less for disfavor
It looks like StrategyWiki have the conditions mixed up, though it may be a bug in the game that perhaps TSLRCM fixes. I haven't checked this either. As far as I know, regarding Zez-Kai Ell, your reputation only changes this particular dialogue, with no further repercussions.
Visquis convo at the combat pit
This is the second and last time your favor with the Exchange is checked, as far as I know.
Optional:
Zez-Kai Ell with alignment check
This is the final interaction with Zez-Kai Ell on Nar Shaddaa. It is your alignment that is checked, and this check would remain as it is, unless you'd like to make an option to check your reputation instead.
Hope this helps. I thought some of it was worth looking into. Many thanks again.