Your bashrc seems to be interfering with it. Can you try with a clean shell setup? In particular, you should not prepend things to $PATH, for example, as that would probably put things from your Ubuntu installation before things from the prefix, and you want prefix stuff coming first.
Well, that’s the whole point of using Gentoo prefix, it “happily injects” all the tools from Gentoo for you to use, and some tools may not be the same as from your own distro. Gentoo prefix depends only on the kernel of the host system (and that’s why it works on all distros), everything else is in CVMFS and is used once you enter the environment. You can actually bind mount /cvmfs into a busybox docker container and use it. But indeed, you may need minor adjustments like the above to your own .bashrc when you use the prefix environment. Gentoo’s less utility doesn’t need eval $(lesspipe) in .bashrc to work. You should just export LESSCOLOR=always in your bashrc (run lesspipe --help on Gentoo prefix if you want to look further into this). This problem has actually come up in someotherplaces as well. Cheers,