If there are consequences, it'll likely be in the case of missed content and narratives, but the 'missed' content part might be subjective since it could just be the missing character not being there for an event. Divinity Original Sin 2 is what I'm thinking of for this.
You might remember
Grymforge Travel CheeseThere was also
Fast Travel Limitation Poll and others I'm sure.
I'm not against the portals, fast travel in service of player convenience is something I'll overlook to a point, but when you start being able to cheese exploration, and dungeon crawling, it becomes an impediment.
I saw someone ask how to reach the Temple of Shar recently, and all I could think about was what might happen in the final version of the game, where someone featherfalls down, finds a portal, and bob's your uncle. There's already a place in Grymforge where you can bypass a party splitting exploration challenge by just cheesing everyone over with the portal.
Hate to say it, but cheese is just part of these games. They're too large and too complex to block all cheese. It's okay. It's a singleplayer game. You just don't cheese if you don't want to. There was a lot of cheese in both Divinity Original Sin games too, same with Kingmaker/WoTC, and same with other RPGs like Skyrim i.e. sneak leveling. The more complex a game is sadly the less balanced it's going to be the further you get into a game, because developers have to account for too many variables for that to ever be possible.