Different branch, and significantly improved.
It's still the same engine. Both Skyrim and FO4 are compiled in the same methods, sharing assets, such as the well noted 'clipboard shield' bug.
The creation engine is already poorly optimized for certain processes. The only reason why Oblivion, Fallout 3 and Fallout: NV were considered 'well optimized' is because they used graphics that were, at the time, good.
Essentially, Fallout 4 is built on an 'improved' branch of the original engine used to produce Morrowind. Although many engine related functions have been spiced up to meet the demand of next-gen consoles, it's still unacceptable that they haven't completely redesigned the engine by now.