If you're separating your application from the core system package manager and shared libraries, there had better be a good and specific reason for it (e.g. the app needs to be containerized for stability/security/weird dependency). If an app can't be centrally managed I don't want it on my system, with grudging exceptions.
Chocolatey has even made this possible in Windows, and lately for my Windows environments if I can't install an application through chocolatey then I'll try to find an alternative that I can. Package managers are absolutely superior to independent application installs.