I did actually notice that her city list was odd when I looked at the file. Since I don't actually make settlers usually I never saw it happen in game. It's a pretty cool idea, even if I'd question the idea of Marisa having a desert city. I assume the mushroom mechanic only looks for land tiles, and doesn't care about actual viability of the land for mushrooms?
The mushroom mechanic actually does care about terrain -- it won't spawn mushrooms on desert, tundra or snow tiles. Forests, jungles, and marshes have the highest probability for mushrooms appearing -- approximately 67%, I think. Mushrooms have around a 1/6 chance of appearing in plains and grasslands tiles.
So while Marisa
can found desert or arctic cities, they likely won't have much in the way of mushrooms.
Also, I actually played on the Arborea map type, the one that generates huge amounts of forest. Perhaps I should have noticed more of a science buff than I did, or I'm just bad at paying attention. She definitely didn't seem unusually strong scientifically though.
A thought regarding the Literature slot in the workshop would be to have it give a tech steal bonus of some kind, like Industrial Espionage in the Autocracy ideology tree. The titular grimoire of the Grimoire of Marisa is her notes on the spells of others and how viable using them herself would be. It'd be even better if it required a non-Forest of Magic work of writing to get the bonus. (Even if you can get that diplomatically.)
There are ways to do that, and it would let me take the espionage element out of the UA to streamline it, so it might be worth considering. It's a bit tricky, since it basically requires keeping count of how many buildings you have that meet the criteria, and adjusting policies to suit, but I know one of the other mod civs (I think possibly the Durrani?) had already done it, so I could probably borrow their code.
By the way, if Reimu's colors are more or less a red/white equivalent of Marisa's then that should be a pretty top tier combo as well. (I'm also trying to figure out if Shinki has the most garish combo that I've seen and I'm edging toward yes.)
For Reimu, I'm planning to go with a wine-red (something like England's red, as opposed to Persia's) and cream (rather like Marisa).
Poor Shinki... I rather like her colors, myself, but they don't seem to be terribly popular.

But Makai does have a lot of freaky colors, so I suppose it makes sense for her to have a rather alien color scheme...
EDIT: As a final note about the initial Marisa test game, I also had Suika active, and big surprise, she did virtually nothing of note all game.
Poor Suika! She's been in my last two test games, and has been a suitable warmonger (declaring war on Norway in the first, and on Greece in the second, as well as provoking all of her neighbours to ask me to go to war against her), so that part of her personality works. But she doesn't seem to be terribly effective at warmongering -- I know in any game with Shaka, I invariably get a warning that someone has lost their capital to him before I even meet him. It'd be nice if Suika could be similar threatening...
She is in the pipeline for an update, though, since I have new graphics for the Kishin and she's the only civ of mine that doesn't use Lua. Currently, I'm looking at giving her bonuses during a Golden Age (in particular, have the Brewery double all of its yields), so that might help her boost growth and military production. Leugi's working on a Brewery UB for his Philistines that is a happiness building replacing the Colosseum, and it has the interesting feature of giving units a unique promotion that increases their movement while the empire is happy, which was an interesting idea. Having Suika's civ encourage keeping your empire happy (and drunken) to gain military bonuses could be cool, especially since the AI has a knack for keeping their empires happy... meaning an AI Suika would be more of a military threat...