I think it makes sense, though it isn’t what you want (or intended) to do.
The limitation is iOS and the problem comes from the way iCloud manages synchronisation.
You can continue having problems, hope for the best, give up iOS (possibly give up Windows, though some entirely Apple users have described iCloud issues), switch away from Obsidian, or switch to Sync. Hoping for the best may work out because surely something will change sometime. There may be an alternative I don’t know, but it is a very frustrating situation.
The usual reason for duplicated files is that a different version has appeared (often by a sync clash) and it’s a way to avoid losing data. I had thought Obsidian had moved to merging files (which has its own problems), but maybe not completely. So again, it’s really down to the sync service.
Many people have described difficulties in getting files out of iCloud too, which it would be essential to do before starting Sync, so you ought to be prepared for that if you take that route.