Hey, in Debian (and Ubuntu) we use --program-transform-name='s/Terminal/xfce4-terminal/' to change the binary name. At the moment (0.4.4) the manpage and html doc folder don't follow the name change. Seems that the following url might help: http://www.gnu.org/software/autoconf/manual/autoconf.html#Transforming-Names
The manpage content is hardcoded to Terminal too (in doc/Terminal.xml.1)
The following is handled now: - Application name in html and man-page. - .desktop file and gnome control center xml file. - Manual location is now handled internally. - Commands in --help.