There isn't a single game on this engine that isn't plagued with bugs and issues that simply are unfixable. Additionally, newer versions of the engine don't shed any of the old problems, but instead pile more complexity on top.
@robot zombie can tell you lots of stories about this.
They ain't fixing shit here, all they do is use newer hardware to keep it going and add more crap on top. That's how you get those massive framedrops in FO4 city center - the engine cannot handle the number of assets in that area well. They don't fix it. They just release a game with abysmal performance. That's why you get 30 FPS limitations here. Its a great way to hide that immense framedrop.
Fun fact, they didn't even manage 30 FPS with FO4 on consoles. 25 FPS was common, and if particle effects happen close to you, you get a slideshow. As if it's 1999.
FO3 was overloaded as well, 2GB limit basically meant no end to the game's problems. 4GB patch fixes most of them.
You're right its quite normal to overhaul and refresh the same engine, they call that iterative refinements, but Bethesda isn't refining it, they're just making sure the Creation ship doesn't sink and leave the bugfixing to the community.