RMQ isn't quite defunct, it just had a fork happen to it and the remainder renamed itself Schism. The Schism project are the ones who maintain BSP2 and the RMQ engine now, until they say otherwise. ijed is the one to talk to.
DP, FTE and DirectQ support BSP2 as well, not the same version though. Havoc wanted a couple cosmetic changes, and as far as I remember these were also agreed upon but not implemented in the RMQ engine and compilers.
In general,
the DP version of BSP2 is the one we last agreed on. <--- !It involves changing the magic bits to "BSP2" instead of "2PSB" and switching to floats for mins/maxs
(leafs and nodes).With maps such as yours (which I assume is huge), there might be performance problems in DP though, according to my experience. Performance is much better in RMQe and FTE. So, like Spike says, build it for the engine it runs best in, and then let other engines support it.
Bundling an engine with your project isn't a capital crime.

Edit: To make myself clear, the way BSP2 is implemented in Darkplaces should be regarded as correct, and the way it is done in the RMQ engine and tools is, at the moment, incorrect since it has not been updated to the latest standard. To my knowledge.