If you actually set the 'upgrade target' of the NLC to Discovery Sphere (in the XML file), it nicely upgrades all tech buildings to NLC's when you research the NLC tech. The NLC can be researched after you have Research Academies, which may actually cause some problems when you make it an auto-upgrade: You can no longer build the research academy, but the NLC costs 300 to build (more than a discovery sphere, which is 250), and the academy is just 150. So if you align with neutral early in the game, this might have the result that you will have to spend lots and lots of resources to build any research building whatsoever on a planet (well, ok, twice as much as on a research academy), whereas now you have the choice between an academy and the NLC.
I don't know if this is really a problem. Like I said, it can be edited into the XML file, it's just a single line.
P.S. the NLC uses a graphic/icon called Museum of Pain. Seems that a lot of buildings use graphics originally intended for something completely different.