This is also the case in retail FS2, unless the issue was somehow specific to just that build (which was a main release, not a nightly).
I've had it happen to me in the retail mission where you discover the NTC Trinity in the nebula (boy, what a mission to lose the comms system--especially since I literally could not warp out as a result, probably because I hadn't actually received the RTB order...had to redo the whole mission...), as well as Aristeia once or twice.
I think the BP team just guardians all of the player's subsystems to prevent any related issues from happening, which is probably a good call. Not being able to call for a support ship to repair your communications subsystem because your communications subsystem is down is pretty facepalm-worthy.