...2. The real problem is with Unity though - you're basically stuck with the first folder layout you pick...
Is that specific to asset store items? Either way is this a reported bug fix I can vote on?
No, its not specific to asset store items - it is just how Unity packages work. Its not a bug, it is like that by design. Obviously that design limits how I can move files around, but it also means that if you've moved a file (from within the Unity interface), importing a new package will correctly update that moved file.
Also about your suggestion, I think you've missed that there are samples specific to the UI, and soon samples specific to the tilmap system, and editor classes specific to each of these. By the time you've added all those, you'd be no better off than you are now
FWIW - in the past we had all the samples in a separate unitypackage in the project, but the asset store guys didn't like that and we were asked to include everything in the project.