Cpanel will overwrite any changes made by hand or other tools for many services that it controls. This alone would make having both on the same server difficult. ISPconfig and CPanel would also have some issues with their expectation of the paths for certain things to be. This could be resolved with symlinks or some other method, but would be a lot of work for a silly purpose. Both ISPconfig and Cpanel are fairly full featured for a webhosting environment. They both accomplish many of the same tasks, but use different methods to do so, such is the nature of *nix.
I like both panels and can see advantages and disadvantages of each. Overall I would say that Cpanel has more features and is a bit more intuitive than I find ISPconfig to be. Thats my personal opinion. That said, I use ISPconfig rather than Cpanel on my own server. I think you would have a difficult time converting someone used to CPanel to almost any other control panel for webhosting, ISPconfig in particular. Cpanel loyalty tends to run deep.