dude, I'm not one of the dev's, but read the code a little: milkytracker's user interface is "hardcoded" in c++ as far as I know. sorry.
so there's no easy way to modify it, unless you learn how to code c++, understand the milkytracker source-code, and have lots of time (lots...). the only alternate user interface is for 320x240, supposedly for pocket-pc pda's small displays.
if you really, really care - take a look at the sourcecode "src/tracker/TrackerInit.cpp" to get some idea on how the interface is built up. consists of manual tweaking almost completely, but when being carefully and investing some time to understand it, you could, for example, swap some buttons, change their text, or redesign the whole interface even. you'd have to recompile the whole program after modifications, of course - giving you a second _complete_ milkytracker version with the changes you've made. subdialogues seem often managed in their corresponding source-modules, but I haven't been really intense on the sources due to lack of time yet to understand them fair enough to give you real advice.
by the way, I also think a more modular, configurable interface-code would be great, also for the input (keyboard bindings etc), but would involve MASSIVE work I guess...like another layer for the ui-setup to be read from configuration files, and some means to edit those properly. would be possible, but involves lots of hacker's manhours...anyway, it's great that it's opensource at all