Hello friend! Created my account just to answer you.
From the start, PID is the Personal ID. It is specific of a pokemon with those IV, that Ability, and that Nature. It is also used (at least in older gens) with the TID and the SID to check if that pokemon is shiny.
Getting the TID is easy, as you can check your trained card and it is there. Getting the SID, however, is trickier. The easiest way would be to dump your save file and check it on PKHex, on the last option of "Box", "Party", and "SAV". The one named "Trainer info" has both your TID and your SID.
Yes, for creating legal pokemon you will need a different program, the one I use to find all the data is PokeFinder, but i do not believe it to have a PLA section, sorry,
Sadly, I got lost with the PID changes on the switch, so I do not know what requirements there are for the legality of a mon on the Switch, but i can tell you that you are right on that last statement, you can't just click the shiny button to make a pokemon shiny, and in fact you wont need it. When the PID of a pokemon and its TID/SID are a match for a shiny, pkhex will automatically show it as a shiny.
Good luck.
