If I understand the question correctly the sort of customization that you are talking about should be possible. Assuming that a kickstart file has been used in the installation additional scripts, like copying files, or asking users questions can be taken care of in the %pre
and %post
sections of a kickstart file. More info on ks files from VMWare.
One could develop a variety of kickstart files for various hypervisor and VM combinations with the appropriate install, and post scripts for copying/mounting VM storage, etc. Menu items can then be added in the PXE server for the various combinations, allowing the user to select the hypervisor/VM combo they desire.
Adding a web interface that allowed users to interactively configure a kickstart file if the one they desire is not immediately available would also be possible.