Reading the SRPMS of the newest xntpd it appears to me that xntpd always binds to all active interfaces including ip aliases. This might not be the wanted behaviour. Eg. named allows to specify the interfaces that are bound to. Now I'm forced to add firewall rules for all the ip aliases I don't want to offer NTP.
In ntp-4.0 (e.g. ntp-4.0.99j-0.1), ntpd will only bind to the primary interface, not aliases. Work is in progress (probably due 4.1) to allow you to define interfaces to bind to in /etc/ntp.conf.