The basis of MariSaku to me is that Sakuya is so removed from humanity in her time serving the SDM prior to EoSD, that even an intruder and thief like Marisa draws her in.
She does shop in the human village, but she's only really there for buisness and her dress and eccentricities tends to keep people from really approaching her willingly. Reimu is a pretty constant human she interacts with, but most every time that happens it's because she's escorting Remilia over because Remilia wants to see Reimu.
Marisa is different. She actively comes to where Sakuya lives and works (even if it is for the books), and regularly gets to interact with her one-on-one. She's clearly taken a liking to her, as seen in both of the good endings to EoSD where Sakuya serves and helps Marisa despite her seemingly not having any permission to be where she is in both cases. Even in the stage 5 interactions, the two bounce off each other rather well in the very eccentric way that they do, showing that Sakuya's off-kilter way of thinking is something Marisa can roll with and play around.
Marisa is the "human" rep a lot of times, but she is very much still an oddball compared to the likes of the randos you see in the human village. Both of these aspects gel well with Sakuya, and i think she really appreciates that and would grow close to Marisa as they interacted further. It's a bit hard to say how much it'd last, Marisa is ever the flirt with many a girl in Gensokyo and Sakuya has her own duties, but I like to think there's a notable spark there.
