IMHO the right way to think of Workbench's DiskObjects i.e. .info files is they are equivalent to the Mac resource forks, where extended metadata about a file is stored. Yes they store icons, they also store arbitrary 'extended attributes' i.e. tooltypes.
The difference is on a Mac, the filesystem hides that abstraction for you and treats the resource fork and the data fork (i.e. the actual file) as one atom. This can be seen not only on CrossMac when reading ancient HFS disks, and today when using a FAT disk on a Mac, where the resource fork is what becomes the annoying ._ files.
But yes it would be nice if more things other than workbench were aware of their existence. Or that perhaps the filesystem could take some responsibility for ensuring they move or are deleted with their 'data forks'.
As for shortcuts and UI, it would have been nice if more apps had followed the AUISG suggestions, unfortunately it was pretty hard to get hold of a copy back in the day I recall, although I have one on my shelf. It is/was totally up to developers to choose their shortcuts so it's on each of them. Perhaps if ClassAct/Reaction had seen greater adoption or Commodore had released their own proper set of GUI controls or even just some complete examples of full features 'document' centric applications we might have all then used as a template. The best example I ever saw was Deluxe Music 2, absolutely it set the standard for how to build a font sensitive, style guide compliant, user friendly, and accessible (due to consistent use of shortcuts) document centric application. Heck, even today I can't think of another app that has a global, floating set of toolbars that crucially, can never itself be selected as the active window - something crucial for free floating 'speedbars'.