You can customize anything, the problem is always how maintainable your customization is. People keep making FrankenDebians (https://wiki.debian.org/DontBreakDebian#Don.27t_make_a_Frank...) using curl|bash install scripts, alternate repositories or just plain brute force symlinking libraries with a hefty dose of chattr +i.

A properly customizable distro allows organizing and tracking patches in layers, etc.