I have run across the periodic application that violates both my quality standards and sensibilities, yet I find indispensable. An example here is the e-reader software KOReader. It makes zero sense as a desktop application since it is designed to run on dedicated tablets hardware with e-ink screens. It is not packaged by many distributions, likely because few people would be interested in maintaining such a package.

So why would I want to use it on a desktop? Because the breadth and depth of features are unmatched. In my case, I am willing to put up with a quirky black and white touch based interface[1] in order to have access to those features on my laptop. So I use the AppImage.

While I dislike the mentioned distribution formats for the reasons you mentioned, some software is so wonderful[2] that it's warts should be ignored.

[1] It does have keyboard controls. In verifying a couple of details for this post, I also discovered that it can be controlled from a gamepad. Connecting my laptop to a television and sitting back to read a book with only a gamepad in hand is something that I am going to have to try one day.

[2] And sometimes that wonderfulness extends beyond features. The lua based portions of KOReader are sufficiently clear that I was able to create a profile for an e-reader (tablet) that is so new to the market that it isn't yet supported in the release version (the e-reader is only about a month old, while release versions of the software come out every four to eight weeks).