how_do_i_do_that I think he was talking about general commercial ROM images, agreed none have proper DLDI autopatching though. That said there is port of the command line DLDI patcher to the DS which works pretty well.
Back on commericial games, theoretically speaking it would not be that hard, but most GBA slot stuff that still exists was a minor step from the old GBA stuff that needed custom drivers and everything so onboard patching or save emulation was never really attempted. For what it is worth the EZ4, which is about the only good GBA cart you can find nowadays, programs work pretty well in WINE and equivalents as long as you make sure to set up a D: drive or tweak the program to read from a c: drive instead if that is your worry.