The "extra" polysilicon region is a capacitor made of silicon and polysilicon. These capacitors were a "bootstrap load", essentially a way to drive a transistor harder to get a stronger output. The capacitors you're looking at are for the instruction register to drive the signals through the instruction decoder (basically a PLA). Since the decoder is fairly large, the signals into it need to be boosted. I haven't looked at this for several years, so I may be wrong about some of this.

http://www.intel4004.com/btstrp.htm