Those are interesting scenarios that you came up with. I'll try to give my thoughts on a few of them now.
If Touhou ended with Mystic Square, none of us here might've known about the series at all. Those games were still niche in Japan, so without any promotion like on social media or with public events like Reitaisai, the series would've been forgotten over time. The PC-98 era does have some memorable music and characters, but the amount of fanworks around then must've been tiny compared to after Eosd.
I think touhou would've been somewhat popular today even if Eosd, PCB and IN were the only Windows games that released. These games have the most iconic themes in the series and UN Owen was her is probably how a lot of people discovered touhou music, including myself. The character designs are also iconic, so I think plenty of people still would've made artwork or other fan stuff related to them nowadays. Back in 2004 though, the touhou hype in Japan was exploding so much that when the first Reitaisai was held, there were over 100 groups participating!
I love the way ZUN handles most of the offical touhou content on his own already. I wouldn't trust anyone else with the series other than him. If he decided to work with different companies though, they could help continue touhou for a long time and bring in more creative ideas. There is still the chance those companies could get greedy and ruin everything. We've seen this in gacha games like Lostword, where they're only focused on making as much money now, instead of respecting the fans and the series. This is usually how a lot of other indie franchises ended up being ruined too.