I think it's Madarame and Saki in the future.

The wife is a non-otaku who dated one of her husband's friends before him. I think she's Saki.

Saki told Madarame that she could see being with him if she wasn't Makoto.

The husband is an office worker like Madarame. The husband is shown to be friends with Hato from the club.

I think this is the future where at some point she broke up with Makoto and then married Madarame.

It isnt, not only do neither of the characters look like saki and madarame but the author himself has said this genshiken and spotted flower isnt connected, he threw in references from genshiken cause that is his most famous work, you basically is playing the fans that want that match up so bad but again he has already basically said it isnt them two, here is the interview
https://www.animenewsnetwork.com/feature/2015-02-03/intervie w-genshiken-creator-shimoku-kio/.84036

This is the question and his answer
What is the relation between your other manga "Spotted Flower" and Genshiken?

Hm? There isn't one.

...And that is my official statement.

The title name was just a playful idea that I came up with after creating the concept of the couple and noticing them feeling very familiar to me. I'm honestly not sure what to do with the big reaction that it ended up getting from the fans afterwards.

Even from the planning stage, there was no intention of making the two titles related in any way. The idea never even came up during discussion with my editor either.