The OS doesn't create the files, the application does. The OS would need a way to track what's being created throughout the lifecycle of the application on the device. For example, at install the app may just put the .app bundle in /Applications and then complete. During first startup, licensing, saving, customization, and at other various indeterminate points the application might create preference files, directories/files in /Library/Application Support, etc. macOS does log things but those get rotated, if you just keep infinite logs you end up using up a ton of space.

Apple could try and require that every Application provide a manifest of where it may put all files, but I don't really now how they'd enforce it and this is still subject to error and may result in the wrong thing being deleted. Also, keep in mind there are some shared folders and file between apps within the same suite. For example, Autodesk puts a lot of things from various apps into /Application Support/Autodesk.

Another thought is, sometimes you don't want it to delete all associated files created. Often applications create a save directory in /Documents. I think SPSS or Stata might do this (haven't work with them for a bit). So if /Documents/Stata has all your work and some automated Apple uninstaller removes it, that isn't ideal. It may even be disadvantageous to remove a plist file. For example if you're installing an old version of an app for a new one, it may use the same plist with your settings so you don't have to reconfigure the app. There's just a lot that can go wrong if you automate this process for what is often relatively little gain.