My understanding is that the actual drones themselves do run a hard realtime operating system. Linux (and formerly Windows) is used to run the workstations on the ground that the drone pilots use.

I don't know about realtime features, but the point of the article, ( not necessarily the point the military is trying to make) is that open source produces more secure software. The power of open source is somewhat proportional to its popularity (in the sense that it is based on the whole concept of "more eyeballs"), therefore Linux is clearly a better choice.

Also, I don't think QNX is necessarily more obscure. It may not evolve on the desktop/server market, but it is an industry standard in its field.

I think it is for the command/control center - or at least that was my take on the article.