Best I can tell, the basic UI resources (i.e. not station or ship related) are baked into the .exe file. Until/unless the devs want to break those out into external scripts, our best bet for doing this is probably rebuilding the whole alliance transfer window from scratch in a separate mod, using inventory add/remove functions like are found in researchstation.lua.
In this case, it's probably better to petition the devs to add the functionality (or, ideally, inventory multi-selection), as it's probably a lot fewer lines of code for them to do it.