Yes, the gearbox crossmember is just to provide a place to put the other end of the jack - one end against that, the other against the back leg on the subframe. Doesn't take much winding. I was a bit worried whether the extensive repairs I'd done on the hatch meant that I'd put an important hole in the wrong place, but then I remembered I'd had to do the same on my old hatch, which hadn't been repaired by me. In any case, the nearside lower mount is one of the few bits of metal on it that I haven't replaced.
I built the engine, clutch and gearbox onto the subframe and slid it under the front of the car, again as it was less hassle and potential scratched paint than dropping it in from above. And I echo your thoughts JP on how much room you suddenly have once this stuff gets bolted back in where it came from. I left the head off as it meant I didn't have to raise the bodyshell any further. Given the shape of the chassis rails, I am nervous at raising it too far as the axle stands are very far inboard.