If the user wants his domain to point on the subdirectory, there are several possibilities:
1) He buys his domain somewhere else, and the isp where he buys the domain has to take care that the domain is redirected correctly. No work for you.
2) He buys the domain somewhere and the ip points to your server. In this case you have to enter it on your server. That's possible with ISPConfig, just enter it als Co-Domain and forward it to the wanted subdirectory