First a quick note on push
First a quick note on push buttons versus toggles. I found spring loaded.center off momentary SPDT toggle switches, so push buttons (for single turnout control) are out and toggles are in.
Now to your questions:
That yard is used primarily for storage, not classification. Downtown receives three scheduled freights a day (and perhaps one extra.) Two are intermodal expresses (one westbound and one eastbound) that could take cars right off intermodal yard tracks (those tracks are one for each of the three other destinations served by the express service, and one for any overflow), except that it'll be faster for the expresses if the blocks are pre-positioned in the yard.( There's a carefully choreographed "dance") to get the intermodals in and out quickly. The other freight turn is from the division point yard. It drops off the local deliveries and picks up all outbound traffic for classification at the DP yard. At best (worst?) the local crews may have to divide the inbound traffic into loads headed for Northside and those headed for Southside.
All that means that movements of cars within the yard will involve blocks, far more often than single cars and with much of the the west end lead serving as part of the runaround for Southside, most movements are going to involve conflicts whenever more than one crew is working downtown (The most planned are two crews). It's planned that way. City acreage is expensive.
(BTW, your example of a locomotive leaving the engine facility and heading for the RIP track doesn't work - both are in the "Blue" zone and would affect only the turnouts within (the west end of) the Blue Zone. Engineer shows up for work, selects his track, runs out to the turnaround, selects the RIP track - only the three turnouts are affected.in total - even though all of those *may* be affected if someone operating in the Red zone want to access the Thoroughfare track (which is also in the red zone).
Any crew working the yard storage tracks via the red zone buttons wouldn't be setting any of the blue zone turnouts.
As for more single turnout switches on the panel, you're probably correct. But they won't be difficult to add as needed. The control panel will have a flip open front and more terminal strips than Carter had Little (Liver) Pills. Drill a hole on the faceplate, insert toggle, solder wires to toggle (no diodes necessary for single turnout controls), screw wires to normal and reverse terminals for appropriate turnout's circuit board and close panel. (check you got the right directions, if not, open panel, unscrew and reverse wires, close panel and check again.)
I'd rather have too few switches and have to add them then clutter up the panel with too many. (BTW, the other two panels - for Northside and Southside - will be heavily weighted towards singe turnout control, rather than route control. Until I get into deep thought, I'm not sure there will be any routing controls on either.)
On splitting the yard tracks in the contol panel diagram, I dunno.... My first impression looking at it is that there are two yards there. I'm thinking more along the lines of changing the text on the panel from "Legend" to something like "Route Start/End" or even "Span of Control". Those are strictly printed symbols, not working LED's or switches.
Mike