While it is true that Gen 8 split shinies to Square shiny and Star shiny, the transferring methods (HOME etc) doesn't limit shinies from older games to one or the other.
In other words, any mons you transfer over can be either shiny. Not a bug.
Referring to the part you had in brackets: you're right and wrong:
You're wrong in the sense that: PID is not a thing for Gold/Silver.
What determined shininess is the DVs, and the DVs were retained when traded to RBY, which is why the same mon when traded back to GSC, retained shiness.
Tho in the sense that you're right: Yup, the PID stays exactly the same. So it could be either shiny, depending on what PID it had at the first place.
Yup. Let's say the raid host was hosting a Gmax Toxtricity raid, and one of the participants had absolutely no badges,
when said participant catches the Toxtricity, it's level (current and met) would be reduced to 20. Also not a bug.
(Note: the levels reduced to, are the same levels enforced by the story, which is the "what level can you catch" level)