So, the whole gag with the ships door and magic flashing was made up by Noel. He explained it to me as her lab doesn’t actually exist in their apartment. It’s just a magical door to her lab, which is on a ship, deep at the bottom of the ocean.

It’s protected by powerful magics and exists as a safe place for her to experiment.

I thought it was a neat idea, so, it’s canon.

Similarly, Phineus has a Fortress of Solitude-style gallery with a bunch of keepsakes and artifacts that exists in an extra-dimensional space. He can enter it through a doorway in their offices. WHen he reaches into his magic pocket, he’s actually accessing that gallery, to pull things from. Rarely, though, he may grab the wrong thing.

His study is actually in their building, but it’s heavily warded and protected.