I've looked at the 6502 simulator closely, but not the Atari simulator. In the 6502 simulator, the "transistor-level simulation" is simulating each transistor b

I've looked at the 6502 simulator closely, but not the Atari simulator. In the 6502 simulator, the "transistor-level simulation" is simulating each transistor by moving "units of charge" around and treating the transistors as switches. So it's not an analog transistor simulation, but it's more than a logic simulation. The reason that the simulation needs to deal with charge levels rather than simply on vs off is there are places where, for instance, a large transistor will pull a line high and a small transistor pulls the line low, and the large transistor wins.