I don't see this behavior.
I downloaded xchat-2.8.6.tce via appbrowser on a pristine state machine.
Of course all the gtk2 tce type deps were also download into the tce directory.
Then, to test, I deleted only the xchat* files from the tce directory, leaving in tact all those gtk2 tce files.
After a reboot, I then went to appbrowser and downloaded xchat-1.2.8.tcz and only that was downloaded.
The download script uses /usr/local/tce.installed to check if an extension is already loaded on the system. If you look at that directory, there is no extension type indicated only the base name of the extension.
Perhaps, I have misunderstood. Please supply specifics that can be reproduced.