...which can be seen nicely here:

https://floooh.github.io/visual2a03remix/

The 6502 CPU is in the lower-right quadrant.

(and here for comparison the 6502 on its own: https://floooh.github.io/visual6502remix/)

IIRC, the rest of the die is the sound hardware.

And the empty upper right corner was a fabrication test structure; it's missing in the simulation because it was completely isolated from the rest of the chip. You can see it in the die shots here:

http://www.visual6502.org/images/pages/Nintendo_RP2A_die_sho...