Hi,
I am running the apache webserver instead of lighttpd on the pi3 with xbian installed. So yes it is possible to migrate using another webserver.
I did not encounter problems with the functionality of the pi-hole gui.
Only downside is, that if you upgrade pi-hole using the update script, it will automatically install lighttpd.
So after upgrading I run:
sudo apt-get remove lighttpd
to uninstall lighttpd.