Linux is about choice
Open Source is about choice.
I run open source software (in my case, Debian GNU/Linux) because of the freedom it gives me - I know that if I don't like one solution, I can install another or write/hack my own.
I know that for this reason I will never have DRM or other "pay us to remove" anti-features in my software. And I am aware that "payment" includes surveillance data for many "free" closed-source apps. If any open source app were to start spying on people, there would be an easy solution involving a ubiquitous piece of cutleryware.
I agree that sometimes packages can be broken downstream in linux distributions, but reinstalling the operating system (even if you count debootstrap/chroot as reinstalling the OS) is never the only option. There's always a way around any problem, that's one of the most beautiful things about Open Source.
Whereas In your pre-packaged containerised world, you remove that freedom from users, by making it difficult for them to fix issues with your software by themselves, and make it more difficult for them to make it work with other pieces of software that you hadn't personally envisaged. But maybe you are flogging some closed-source, DRM-infested spyware/crapware and you don't want your customers looking too closely at what you are doing on their computers - In which case you are on the wrong platform mate, you can go and take a Running Jump.
Rather than force users to have some god-awful containerised linux system like Snap or Flatpak (or worse, Android, which just bungs a JVM on top of Linux and hides away the workings completely, and actively punishes users for trying to build applications from source - oops, you have debugging enabled - safetyNet failed, no DRM apps for you) I would prefer to educate and encourage users to build apps from source, so that they can understand how the system works, fix bugs or add missing features themselves, and contribute to the community project that they are using.
If I really don't like something in a Debian package, or some version that I want has fallen out of compatibility with my system packages, I can always run apt-get --build source [package], and fix it myself.