I'm sure it's because they aren't looking at the series as a continuation of Gotham and they're not looking to make sure they match up with it. Sure it's using certain elements like the skyline (wouldn't be surprised if it had more to do with laziness) but at the same time it's acting like its own thing. It's much easier for me if they're different worlds. Especially when we don't have confirmation it's meant to be the exact same world.I'm very curious how they will or if they will fill in the blanks for the Court of Owls inconsistencies(?) as the season goes.
I feel like maybe the characters are still learning as much as we the audience are, and more backstory will be given to us that lines up more with what Gotham established.