"I was told a while back that these front ends (Esim at that time) wreak havoc on the file system and makes it a nightmare when doing installs and other system level admin outside of the front end. The person also added that if I was to require a server move back to a plain RH server, it would be an issue since scripts may have to be corrected for file paths. How true is this?"
Ensim currently only supports an older version of Redhat.
Once you go Ensim you cannot go back. Only way to get rid of it is to nuke and pave the machine.
Ensim gets it's fingers into everything. Updating one component on your own breaks everything unless you really really understand how the Ensim system is built and are willing to take a lot of time to do the most minor updates. From that point on you're on your own. You'll not be able to use Esnim's updates any longer.
I have not tried CPanel. I'll bet it is not vastly different.