So either have a completely separate install or recompile your application from source (which assumes it is open source and you've got the build environment correct). Gee, isn't that convenient?
Like I said: try to color outside the lines and all that fake ease of use stuff goes away and you have to deal with the garbage pile of a system underneath.
I don't want to go down this road but it is easier than how you make it out to be. For example matlab can be installed in $HOME even though it is proprietary because the install script takes that into account.
I got frustrated by the Windows updates and app updates that I am willing to put in that extra effort once to install something and then forget about it than try to fight the system on a daily basis.
Proprietary application developers pretty much have to do that, because there are no standards between distributions so they have to remain flexible. OSS developers don't bother because, hey, you can just recompile from source! Not that that would actually make your application portable, mind you, you'd just have different hardcoded paths.
If there was a standardized base system and AppImage was embraced for deploying applications, that would make all application developer's lives easier, proprietary or otherwise, and all that wasted effort maintaining out of date applications across distro-specific repositories could stop.
Like I said: try to color outside the lines and all that fake ease of use stuff goes away and you have to deal with the garbage pile of a system underneath.