Hi Noopy, I don't think I agree with your comments about substrate grounding
The substrate has to be the lowest potential in the circuit, with few exceptions*. Otherwise unlimited current would flow from the P type substrate to any of the random N type things (like NPN collectors) made in the N type epitaxial layer.
I think the brown areas are plain, unmodifed N epitaxial layer. So the "thing" connected to pin 1 is simply the whole reminder of the epitaxial layer which hasn't been separated into transistor tubs by the violet isolation diffusions.
Isolation diffusions are P type and they go all the way down to the P substrate, so we see at once that the substrate is electrically connected to pin 4 by the ring of isolation diffusion separating Q1 from Q2 clones. There appears to be yet another parasitic diode not included on the schematic, from pin 4 (substrate/isolation) to pin 8 (Q2 collector). You could detect it with a DMM.
Nominally, pin 4 is Q1 base. Of course the substrate can't be the base, the base has to be located under the emitter. There are actually two concentric "emitters", the outer one is the zener cathode. Interestingly, the base has no metal connection on the surface. Instead, it appears that there is a hidden column of P type material extending from the base all the way down to the substrate. This is the reason why pin 4 is connected to the substrate. Not sure what's the point of that, perhaps voltage at the bottom of the base was more stable than at the top
Q1 collector tub is another part of the circuit with no surface connection. Instead, it's connected from the bottom with four deep "jumper links", which might be made in the N+ burried layer, embedded in the substrate below the reach of the isolation ring. It seems somebody worked very hard to make Q1 collector current flow "upwards" through the base and stay away from the surface for some reason.
*exceptions: some emitters are one diode drop lower potential than the substrate, because they are located on bases whose potential is equal to the substrate.
edit
Now is time to power that puppy up and see if it still works
(BTW, if anyone actually wants to try that, cover the IC from light. Light will cause unwanted conduction through reverse biased junctions, perhaps even damage).