I'll consider this a bug, after all, it doesn't make sense to use the portal if it doesn't work with the train schedules. All scheduled trains ignore the route with the portal if there are other routes, even if the portals are on the same planet.
If there is only one path and portals on that path, the trains will be routeless, stopped in the middle of the tracks.
I think I understand what you mean. You want trains to automatically go through this door, right? If so, the module needs to monitor any train timetable changes, which is a significant performance overhead in the game, resulting in substantial UPS losses. If that's what you mean, I don't plan to do that. You can manually set up an interrupt mechanism or something similar to solve this problem, or set a fixed route. If you're using Cybersyn, another module of mine has this feature; it's compatible with Cybersyn and can automatically transport across the surface. However, this module doesn't currently have that in mind.