Fedora has too, and doesn't have any issues.

Considering Debian is the only one that hasn't just switched, it does sound like a mountain out of a molehill for package manager breakage.

Gentoo still uses the split setup by default. Unifying the directories is currently a work in progress and will eventually be the default from what I understand.

It's possible that Gentoo will still support the split setup even after the default is changed since it supports many different inits and libcs but I am not sure.