Actually, you can argue that they are still limited by what the engine can do - which, in turn, means it affects game design due to the fact they might want to implement an idea, but either they would need a hacky way to do it (like trains in Fallout 3 being a fucking equippable hat with an NPC running underneath the map, which is probably why their Fallout games don’t have drivable vehicles) or simply cannot due to technical limitations of the engine.
This is like saying a good wood carver can still be good if they have shoddy tools, when the reality is that a good craftsman is only limited by the quality of tools they have. If I can’t fully realize my wood carving because my knife is too blunt and do the best I could with what I have for an inferior design, is that my fault or the tool’s fault?
Two things: 1) You’re making it sound like swapping engines is incredibly easy (it’s not, and you have to train staff on how to utilize it from the ground up and that can take a while), and 2) you’re probably right on why they keep using CE, and the sad reality is that Bethesda absolutely intentionally designs uncooked barebones games because they realized they can just have the fandom make actual interesting content, or QoL changes. They also know that ~~Creation~~ Gamebryo Engine does limit them a lot to what they can do, but rather than going through the cost and time of changing over engines, they just let the fandom create the script extenders that are available for literally every single game of theirs since Morrowind so modders can literally do things the base game can’t let them do.
So this is more of a case where the craftsman has shoddy tools, but they don’t care because they’ll churn out a piece-of-crap and have their audience improve it for them for free. And then the craftsman will have the gall to try and get a cut of the audience’s work somehow.