Is it possible to complete those maps if your character started from Klaipeda? I can’t seem to access areas such as the Hidden Chamber on 1F and the Penitence Room on 3F.
I understand this is because due to my starting town, I don’t have the main quest line needed to unlock those parts of the map.
Am I doomed to have those maps unfinished? 
Definetly no. I’ve done lots of quests from both cities regardless of the starting one in more than one of my characters. What you might have to do though, is go back to the starting map for Orsha, Lemprasa Pond and start the main quest line for that city. Go on completing those quests until you catch up to your desired map. That way you should have full access to all maps. If you feel like completing the side quests too it is up to you 
I hope it has helped 