That's an insightful question. 
Tying AC common and DC common together can seem like black magic or something untoward! But here's what's going on. Remember we are starting with two isolated circuits...the AC circuit which has the track power and the DC circuit which has the timer/relay power. These two circuits are isolated because they are operating off separate transformers. Hence they are not aware of each other's existence in an electrical sense.
As you know the term "circuit" itself implies a to-and-from. Connecting one wire between two isolated circuits does not create a new circuit or electrical interaction because you only have a "to" and not a "from". Hence the two circuits behave independently as if the other was not there...like two ships passing in the night.
So that's what we have when with the shared AC and DC commons. The AC circuit can have a bell and/or whistle DC offset, it can drop to 0V on the track (for direction change) or even jump to 100V AC or whatever and blow up the engine, etc. … but the DC circuit is completely isolated and ignorant of this action!
I don't know if this made any sense at all but that's how I think of it...
