https://www.reddit.com/r/pokemonrng/comments/2fa5wa/unown_shape_map_of_pid_75d56cb1/
This discussion was happening a while ago here, I think
Thomaz managed to get 27/28 Unowns with a single PID?
TL;DR : Determined by encounter slots, which are determined by which puzzles have been completed (order doesn't matter).
Actually, I'm not even sure you can say it's determined by encounter slots. I'd argue they are completely determined by which puzzles you have completed. You won't get a different Unown if you try a different frame with the same Seed. Generally, you get letter "X" by normal means, then letter "Y" by using the Mysterious Transmission.
I haven't tested everything, but the thing that worked for me, is to use some sort of back up before you complete the puzzles (so, emulator is the easiest for this. Redoing a file four times would be kinda annoying...).
Remember how the Mysterious Transmission helps you find Unown you haven't seen yet easier? You can use that to pretty much find them all (except ? and !, they are exempt from this rule for some reason...).
Let's say we complete the Ho-Oh puzzle and only this one. That unlocks
W,
X,
Y and
Z. Say that the normal try gives up
Z and using the MT gives us
Y. You catch both of these, then save and reseed the game. Now, if you use the MT again, either
W or
X will pop up instead of the
Y we got earlier. Say
W appears, we catch it and then, when you save and reseed the game again,
X will now appear, while using the MT.
You can do this for every puzzle. Hope that helps. :)
Edit: on another note, I just RNGed a new save for the
I was missing. It worked. :D I now have a full collection of shiny Unowns (though this one has higher Atk. <_<).
Edit2: now that I think about it. You might actually be able to do it in one file if you keep catching the one that shows up while using MT. Like, have all four puzzles active, then catch whatever shows up, then save and try again. I don't know for sure, but I guess it's worth to try. :)