What this idea forgets is for example, that I can setup such skip-condition for all train stops. What then?

That is true that i forgot about that corner-case. I would make it mandatory to have at more or equal of 2 stops in the schedule and at least more or equal to 2 "non only-if" Stop to ...

TL;DR
Make Stops in the Train depend on specific dependencies in the train.


What ?
Imagine a base where you have a trainstop only to refill gas on your trains. I though it where cool to have a only stop there if you have "more than X units cargo" or "less than Y units fuel" or something ...