Nowadays, yes. Go back 15+ years, the registry was used extesively.
My reasoning as to why, Linux was never a targeted platform for software back then, now it is. There was only GTK back then and it didn't look "nice" (appealing) at all. Plus GTK apps were huge for Windows, since you'd have to also install the GTK runtimes and all that... that just took a lot of disk space, which was expensive back then. Compared to an app that does the same, but spends only 10% of the disk space needed for GTK (you could even go a lot lower with compressors), it's obvious why GTK was never a viable option when making a GUI app.
And since Linux doesn't have a registry (or even if it did, it'll probably be completely optional to have it or not, so you can't rely on users having it installed), you'd have to just save the settings in a file, just like the rest of the FOSS applications. So, it makes no sense to have completely different codebases for the same app for Windows and everything else. In fact, most apps nowadays that aim to be cross platform just use Qt. You can compile it for watever you like, there is no need to keep separate codebases.