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.
* How do you know if the base silicon is N-doped or P-doped? (does it matter?)
* Why are the layouts of NPN and PNP so different? I’ve seen many die photos and you can (usually) easily tell which transistor is which.
* Lastly, are there any guides on learning how to decipher a die shot into a “schematic”? How do I know which colors mean what? (they vary between IC)
(if it’s not obvious, I’m still learning about this stuff)