I don't see why it would be that annoying. I use Firefox on my phone and desktop, and things sync just fine, so I don't see why throwing Windows into the mix would matter. LIkewise for things like Discord, you just login and you're good to go. I guess if you install something in one place you need to do it in both, but that's a one-time thing.

For me, the most annoying things come from the Windows side. Windows likes reboot during updates, and since my default is Linux, the next time I use Windows it inevitably needs to reboot a couple times before I can do anything. That's a really crappy user experience, especially since I only boot into Windows like once/year. If I used Windows more, it would be less of an issue.