Eh. I personally prefer that if I'm going to add any new code in to the process (which Ultrasound does do), to stick it in a DLL and have that injected somehow. Yes, it requires the user to either run the game through a launcher, or inject the DLL via Aali's driver or similar, but frankly I expect the majority of users applying mods can do one of those. Bootleg installs Aali's driver automatically after all, right?
Seems far cleaner to me to put each change in its own DLL that can be easily upgraded, changed, or removed, and automatically avoids overwriting the data/code from another mod (unless they're both trying to change the exact same thing, I guess - but there isn't any possible solution in that case).