UFO Extender is just a runner, it's not a game. And vanilla xcom is optimized to run on 20Mhz intel 486SX. Not surprising it runs so smooth on modern hardware.
About Battlescape:
In Vanilla the only calculation for each step they are making - is Unit-Unit spotting (which is quite fast). No need of such fancy things of OXC like each step light recalc, area discover, fullscreen rendering, which are quite CPU-heavy.
Vanilla rendering, by the way utilizing re-render of "invalidated" screen areas (not full rerender): did you notice, that all animation stops while your dude is walking? But after reaching destination point they are making all necessary area and unit revealing (in the hindsight), and lighting switch from old to new location. Quite frankly at this moment vanilla slightly hangs.
So this is simply side-effect of more modern fullscreen animation and dynamic area revealing.
Geoscape shouldn't run any "choppy". It might be caused by some OS overload with another tasks of higher priority.