Isn't it for the most part a non-meaningful choice then? It sounds like either your cult will be obviously better for you, like the Mechanos cult for the mechanos, or else you'll always be better off going with one of the tried and true religions.
Or will the cults be going for a weaker but more specialised role? You mentioned the Cult of the Emperor would increase diplomatic relations with the Scions, - is that almost useless (but believably useful every now and again in certain games) bonus intended to make it a meaningful choice every 1/100 games, and otherwise a sub-par choice that you try to avoid compared to a real religion if possible?
I raise the issue because - for the most part I find that more options is better (more civs, more civics) providing that balance is maintained - in this case though it seems like you're intentionally going to be balancing some of the options to be worse than others. (Cult vs Religion).
While at the same time trying to make it so that (Guild vs Guild) is as balanced as possible so that the choice for which guilds you want active is important.
To be honest the way you write about the guilds currently sounds like a much more interesting interpretation of the base mechanic. The mechanic being of things you adopt which multiple teams can have. The religions in this mod with unique units, spells, heroes and civicis are done much better than base civ. (Your old coperations that I'm glad you're doing away with were done just the same as base civ and so not paritcularly interesting).
The guilds you're planning sound like they're taking yet another step into making meaningful choices and effects. I could easily see them overshadowing religions in terms of interest, mechanics and overall effect on Gameplay. So far the only thing that the religions have that your new guilds don't is diplomatic relations effects (which guilds easily could have, since civics and religions do).
What I'm saying is I think that the cults may be a lot more interesting than the religions and it might be worth (perhaps in a future patch) considering changing the religions to have more interesting and varied effects.
For example: although it doesn't make sense for the holy city to change the way the guild headquarters is planned to change - the ability for the centre of power to change in a game makes the guilds much more interesting and less static. As a mechanic for making varied and interesting games (single or multi-player) it's much better designed. A possible addition to religions would be a centre of worship (different from the holy city - the way Bethlehem and Jerusalem aren't Vatican City) - which was able to move to allow the religions to keep up. (All of this stems from my general belief that missing any/all religions in a game essentially drops you out of the religion game entirely because they're so focused on the holy city - although the mod fixes that somewhat with the unique units and civics - however all of that basically makes you get one religion and stick with it - or else one religion only because a late game religion is yet to come).
Alternatively you could try to make the differences more pronounced so that religions and guilds served very different function. As it is, I could easily see the guilds being more interesting and eclipsing if not the importance of religion, at least the interest and some of the fun of them. (Albeit only by adding a better more fun variant
)