Hello @HarmjanK. I’m fine too, thanks!
Technically, you are right and “Onde é a estação de trem” would sound more correct and should make more sense to someone studying Portuguese. That’s why I’m fixing it right now.
Anyway, just for your reference:
I probably instinctively opted for “Onde está a estação de trem” because, in this case, we are implicitly using the word “located” (“localizada”) just after “está”.
So, the phrase should mean: “Onde está localizada a estação de trem” (“Where is the train station located?”).
I know the temporarily x permantly issue would still be confusing here, but we do say “Estar localizada” much more than “ser localizada”, even for fixed things like buildings, addresses, etc.
As another option, we might still say “Onde fica a estação de trem” (which literally should mean “Where stays the station of train”). That’s very usual as well.
Well, I hope this may have helped you (and not made things more confusing! =P)
Let me know in case you have any other questions.