I have no modding background, but based on the usage case I can suggest that it might be a good idea (even beyond the scope of this mod feature) if you simply installed dedicated stops for each train. How you name them, if you choose to assign them the same name, if you control with smarts, or if there is a need for a parked train to be loaded / unloaded / fueled / repaired, etc., sounds like it would influence what the final product of multiple individual train stops would look like, but I am not sure of any reason that would make it impossible.
Context: I run LTN, which relies on all LTN-managed train stops to have unique names system-wide. I have some vanilla / non-LTN stops for exception cases, and I suppose that assigning some of those stops duplicated names (so long as they don't duplicate an LTN stop) would probably be ok as far as the mod is concerned, but I decided it's easier to simply apply the same naming rules across all stops regardless. Not sure how doable my suggestion is in your map.