I am curious if even just a minimal part of it has anything to do with MigSwitch.
If the MigSwitch is really emulating a physical cartridge perfectly and the Switch can't detect it... it can be an issue for a new one, either because they use the same cartridges/security for the new games, as let's be honest I don't see why Nintendo would need a new physical cartridge for this revision, at best a tab like in the 3Ds to not allow them on the old Switch.
And even if it does not affect the new games, the retrocompatible games could be affected and be playable by it.
So some changes could be required physically or by software.
I got all the rest and I see your issue with wanting to sync only individual files. But I didn't quite get what you mean with this: "...that the user can’t enter". You can enter and copy/move/edit files... I cannot understand what you meant with that.
Regarding the sync thing, I am not as annoyed by it as much as you seem, and my use case probably was different, but in case it helps somebody what I opted to was to use it as a disk and use tools that work with disks, so in my case although other tools could be used I use FreeFileSync to copy files from the Drive to a local drive and viceversa. Mostly for backup purposes.
I would be tempted to say in some cases it is even better as in the past you needed to to use their APIs or use their tool to setup those specific sync options and now I can use any tool that works with copying/using normal files.
That said... for other environments like a server or similar, then you are back to RClone and API auths or similar to do actions on your drive.
This is me just nitpicking, but you can flag folders/files to be available offline and it will keep a local copy always, but it will be in their drive thingy. So you can access it even when offline but it's not copied outside their virtual disk. It's just a right click menu option.