It is also a branding problem, imo. Part of the reason I prefer software from distro repositories is because those conventions the distro maintainers enforce he

It is also a branding problem, imo. Part of the reason I prefer software from distro repositories is because those conventions the distro maintainers enforce help ensure that packages won't do stupid things and break my system. Especially with DEB and RPM, where the packaging format supports arbitrary hooks that run as root, this is a big deal. High quality packages that meet distro standards will inspire confidence in customers' sysadmins. Substandard packaging may do disservice to your core software's brand, if your actual software is more solid and thoughtful than the packaging.