We have a svn repo (ask in the irc channel if you want details). Regarding the tracker: this is a community project - feel free to set one up if you think it will be worthwhile.
Personally, I think the bigger problem is the lack of developers willing to add new feature requests (bugs are normally fixed fairly quickly).
There are some command line switches for the SDL version (documented in readme_unix I think). The one you might like to try is:
./milkytracker -bpp 16
..which will configure Milkytracker to use a 16-bit screen resolution. You could also try the values 24 and 32 (I can't remember which one MT defaults to).