The book "The Art of Analog Design" discusses the layouts of components in detail. It says (p280) that theoretically you could make a PNP transistor like an NPN transistor in reverse, but the characteristics of the dopants don't work well for this. Boron diffuses rapidly so it doesn't work well for a buried P layer. And boron only has 1/3 of the solid solubility of phosphorus. The other issue is that the mobility of holes is only 1/3 that of electrons in silicon, so there's an inherent disadvantage for PNP.

I'm kind of guessing that the substrate silicon is P-type since that seems to be more common. As for the colors, each IC is different. There are charts relating colors to thickness, but that doesn't really help me.

N type and p type have different resistance so to get a balanced transistor you need different area proportions of each. If memory serves that is.

Holes have lower mobilty than electrons, so P-doped areas must be larger for the same equivalent resistance.