I think you then need/want to run all these scripts via root shell:
/scripts/initsuexec
/scripts/fixallcartswithsuexec
/scripts/fixmailmanwithsuexec
/scripts/fixoldlistswithsuexec
/scripts/fixsuexeccgiscripts
/scripts/postsuexecinstall
/scripts/phpopenbasectl
/scripts/chownpublichtmls
And of course in WHM:
Security --> Tweak Security --> Php open_basedir Tweak --> Configure
Enable it.
Exclude the hostname of the server if you allow your clients to access their web space via
http://hostname/~username/ before their domain propagates. If they use the IP rather than the hostname - you shouldn't need to exclude the hostname from protection.