I'll give you a short answer first which is basically "unfortunately not, but actually sort of yes", then my general thoughts on it below.
There's two situations in which tnfp won't resume its schedule, firstly if its a redispatch to a destination already in the trains schedule (at which point it continues to that station), or if at any point the trains switched to manual mode. Theres an input control under settings (which isn't defined by default) which will switch the current train, or one thats just arrived after dispatch to manual mode.
So whilst there's no option to have it wait, if you bind the manual mode hotkey and use it to switch the train to manual mode before getting out -- the train will then remain there until its next summoned.
The blank station thing is a bug that came through during 0.17. In short tnfp checks its successfully saved the trains previous schedule before it restores it -- but partway through 0.17 an empty schedule changed from an empty array (which passes existence checks) to being "nil" (which does not), and empty schedules then failed the validation check. I can take a look into fixing that by adding some explicit marker for the schedule being saved as blank.
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Personally its something that bugged me too -- the manual mode switch was a way to solve the problem after a fashion, as I've been thinking through the "right" way to add this kind of functionality.
In my current playthrough its generally about 50/50 whether I want the train to wait or not -- so a mod setting didn't feel granular enough because either default is still likely to be the "wrong" decision sometimes. It'd be possible to add it -- but I'd prefer is to make it more of a dynamic choice if possible.
For a railtool/temporary dispatch, selection tools have a concept of "alt mode" -- at first glance they didn't seem to be exposed to the event api that fires on selection though. For a station select dispatch its do-able, its mainly just a question of what the UI looks like and I'm still mulling that one over.
Any thoughts or suggestions though, feel free!
Cheers, Lee H