Also, sorry for all the questions, but what is with the pwell layer in magic? The entire substrate is pwell without any doping, right? On some things, like the generated nmos with guard rings, I am seeing pwell drawn. But transistors without the guard ring do not have it. If I delete the pwell layer no DRC errors are thrown. It also shows up on the substrate taps for the standard cell library. Is this some drc aid layer or something?

Magic will treat "space" as equivalent to "pwell". But there can be issues with knowing when there is or isn't substrate under a device, such as when the circuit is in a deep nwell region. It is an extraction aid, not a DRC aid. It also doesn't really help much with the deep nwell issue. I have a development branch of magic where I'm working on that, but since it currently crashes magic on some extraction runs, I'm not ready to push an update yet.