Tell that to the users, who will absolutely bitch and moan and berate. Have you ever done user support?
Although I personally despise iOS squircles on Mac, my newer Mac apps do have squircle icons, not because I want them but rather because users want them. They hate when app icons are "out of place" compared to all of the others on their system.
I think the automatically generated icons for your apps look completely fine. And basically all of the examples you showed. You could remove the border on Bonjeff or add a background color to Underpass (or any of them) if you really wanted. If I had StopThe* side by side in my Dock, I would probably wish the octagons were the same size, but they might not have been to begin with?
(My favorite icons might be in Books.app → Book Store → Sections.)
This kind of crap is an example of the worst of their hubristic tendencies.