Title. Is it due to being a more desirable record or is it truly faster due to something in game?

It wasn't until 2018 that people started trying to optimize categories other then The Boss Extreme. The entire history of this game as a speedrun up until this year was on TBE.

I'm assuming you only looked at NG and not NG+, becuase If you check NG+ you will see extreme is not faster. In fact its slower by maybe 15 seconds minimum due to extra menu management being required and additional guards. Additionally NG+ is innately faster then NG by about 7m, so most of the activity is located on that front, plus no one runs any NG runs besides for Sparty and Jaguar, the two names listed under extreme, and even then I think both may have stopped for now anyway.

So the main answer is, because no one is focused on NG non-TBE runs, which is arguably more desirable because you can earn the Big Boss emblem, which, even though it's slower, its looks cooler.