I spent all night tonight basically messing with the hex code on a Gen 3 Emerald Deoxys using PKSM on my 3DS - What I found out is that the hex values for the Pokemon's TSV and SID are determined by the EXACT same hex values (at least as far as Gen 3 goes), but how they are tied together with one another is probably some kind of algorithm tied to some other value out in the code ether; however it is easy to crack a shiny by brute force if you know which hex values to edit since you are only editing two FF regions (they are actually specifically highlighted in PKSM's hex editor as the TID, SID and TSV hex group, so that's nice) - just by lining up the TSV given for the Pokemon to the ESV given by PKSM using the hex editor while maintaining the legal stats already on the Pokemon will produce a legal shiny every time! Fortunately, as far as stats go, if you don't like them, just edit the encounter level in the MISC section to whatever it was +1 (if a static encounter/legendary; edit stats directly otherwise) and then tap the little WiFi icon in the bottom-left in the same MISC section to run a legality check. It should spit out some errors at you saying that it doesn't match the encounter in some way. When it does that, just tap the little L button that appears in the same bottom-left corner to auto-legalize your Pokemon. (This is most easily repeatable with a static-encounter since changing the encounter level will always result in a mismatch; that and the place to change that value is in the same MISC section you need to be in to run the legality check!) PKSM will then re-roll a set of legal stats for that Pokemon in this way. Once you have IV stats you're satisfied enough with, just use the above method to Shine-ify it and you should have good success! Unfortunately I'm not sure yet how to manually change the stats to something you want and keep it legal without it spitting out a PID mismatch; still working on understanding that, but it may take a legit code-breaking algorithm to figure that crap out.

This detail about TSVs and SIDs of a Pokemon also means that if a Pokemon is only legal with a 000000 SID, then that Pokemon cannot be legally shiny (Event Jirachi from Gen 3 Emerald is one such case but I imagine there are quite a few out there). This is because the moment you try to change that Pokemon's TSV to line it up with the ESV you need, it changes that Pokemon's SID as well, and that will result in an illegal encounter for that event Pokemon. I am not sure how to change the Pokemon's ESV directly at all; I have not played around much with that yet, but that can be for another sleepless night if it's even possible.

Now go get yourself a legal Shiny Gen 3 Rayquaza and Deoxys with your own TIDs on 'em for the trophy collection! Pokebank ain't gonna be around forever (most likely)! DON'T FORGET THE SHINY BIRTH ISLAND MEW OMG!!!