When I built my recent version of Chicago, I tried several times to come up with a good system to signal Alton Junction (as well as the interlocking north of Chicago on the MILW and C&NW lines, and all of the stations in general), but unfortunately, the interlockings are too complex to come up with a good system. I think the main problem with Alton Junction is the fact that you have to have all of the double slips in such a short proximity to the diamonds, and that might mess with the system. The AI goes crazy with all of the signaling, and the double slips complicate things even further. Don't even get me started on Englewood, the C&WI yard, and the IC/NYC/RI/B&OCT/STCAL diamond up above the approach to Dearborn Station. It's just crazy! The ATSF facilities next to Alton Junction are also tough, especially the loop track around the servicing tracks and the roundhouse crammed in between the IC line towards Central Station and the NYC/RI/NKP line towards LaSalle St. Station. Also, don't forget the holding tracks between the C&WI leads to Dearborn station and the Chicago River. Those were there in the 60's, but they were majorly overgrown and run down. Also don't forget the crazily curved B&O tracks leading to Grand Central Station with all of the interchange tracks spinning off to connect with the myriad other lines intersecting in the area.
But yeah no, the AI is gonna go crazy. I don't know of a way to signal it and not have everything go all haywire.
EDIT, also, one thing. The streets there wouldn't be sunk below the ground because of the proximity to the Chicago River, which that factory would be somewhat built over (if you included it), the tracks are slightly elevated above the river, and the roads are close to water level. It also seems a bit stretched. The C&WI tracks should be closer to the IC/ATSF tracks since there's a set of crossovers right behind the camera that allow ATSF trains to access Dearborn Station. Everything in general seems like it should be closer together and more congested.