I saw a post here yesterday, and have run into an issue of my own as well. It seems to be a known feature that bi-directional tracks are always exclusive (and I'm sure the logic is really difficult to change at this point) however I've managed to run into a semi-deadlock as seen in the picture.
The main issue is that since all bidirectional tracks are exclusive, they form a single zone, which can only be separated via bidirectional slip lanes. There are cases when this isn't really solvable though. Here I've really designed myself into a corner. There is a station that's supposed to be used by the 2-4 and I've made another one for a 1-2, and made a slip lane.
As the picture clearly shows, this slip lane is supposed to be used if the 1-2 is parked (waiting for a destination to open) and the 2-4 uses the top station and needs to leave. The exclusive zone however isn't broken up, so everyone stays. With chain signals this normally isn't an issue because the track to the bottom (going outside of the screen) would contain a free block, and thus a free route. The first one going into that one would occupy it for however long it needs to, then the other one gets to enter when it returns.
Here however, the whole junction and the bottom route is a single block, and the 2-4 will never get a chance to enter it, because 1-2 is inside and will stay inside even after leaving the station only to return to this exact state.
The only solution I see is to have a bypass lower on the track, wait for 1-2 to leave, enter the bypass, wait for 2-4 to finish, and return to start the whole process again. This inherently links the two train schedules together (meaning 2-4 only gets a go when 1-2 does) which isn't what you'd want from a dynamic system.
Sad as it is, I see the reason you guys made it this way, this very junction would not work if the base state of exclusive zones weren't what they are, and junctions broke them up. They'd of course meet between either 2 the 3 junctions.
However, being able to override the system as a player is essential, so that's what I'd like to ask for. There is a reason we can call back trains for some measly unity cost, we should be able to make mistakes. Otherwise, I'm afraid it's back to uni-directional and two track based systems for me, because I can't have unexpected logistical issues that take in game years to fix and / or a lot of unity.
Save attached if you'd like a gander, COIExtended was used.

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