It is indeed possible to make a nice container that contains a program, offers a clean interface to that program, and doesn’t package a whole pile of largely irrelevant, guaranteed-to-be-quickly-outdated crap with it.

But being possible doesn’t mean that anyone does it. Most containers I’ve ever seen are big messes. Possibly GPL-violating messes if the payload isn’t appropriately licensed. Certainly maintenance and provenance disasters. Unquestionably not reproducibly buildable and possibly not buildable at all.