I don't think it's terribly likely that Nightdive does a port of Quake 3 for modern platforms, given that their work has largely been focused on obscure single-player titles; Quake and Quake 2 are the only real exceptions to that, and even those ports are most likely to have a single- rather than multi-player legacy in the long term.
Also, working as directly with Bethesda as that would immediately open up questions of legality that, especially with how things in the games industry work these days, would most likely result in a quick "no" at best, and a "you need to end your project right the frick now" at worst.
The better scenario, should KEX compatibility ever actually become a concern, would be for someone on their end to approach Wirehead about making sure the mod works with such a version, much like they did with various MegaWAD's for the Unity port of Doom. And while I won't presume to speak for Phoenix, being the only workhorse (work...bird?) of the project at this point, I doubt such a thing would push forward without some amount of actual compensation... and even then, I have my doubts.
