That's not even close to what he stated.
First of all, there is timelines. He posted a graphic:
Games are in the order they will be released.
He stated the only non-canon story was Officer Chloe's as it was a crossover. Everything else that happens is an "alternative universe". The only part where it matters Ayame got the marriage ending is for other games. Every route in the game right now is canonic but seen as alternative endings and they will all have multiple endings by the way. They are canon, they are just not the ones that lead to other games.
I asked starke personally how that worked in terms of other games. If they also have a "canon" route and the others are alternative. He said yes. The second game will also have NTR. If you follow the NTR parts it will be as if Ayame also followed those routes. If you follow the canon route (spies dismantling the drug slash prostitution cartel) it will be as if Ayame followed the marriage route. Routes tie up. NTR with NTR. Virgin with virgin, etc.
Apparently this is only relevant in the fifth game where you will have a party with all the MC's and a new not yet revealed one. I guess to a lot of people this is overambitious but he stated the other games will be much shorter in comparison to this one which come next patch will have breached the 100 original CG's.