They're not, but when you're stabbing the whole shebang, that does add difficulty. If you were to install the engine with the bellhousing, you'd get those four bolts tightened easily, then you could install the transmission.
You went a different route, and nothing wrong with your approach, but because you have everything bolted on, you have cantilevered weight(tranny) fighting you. Support the tail, and wriggle it all into position, leaving no weight on the engine mounts or bellhousing mounts, let it sit above so you can start the four bolts (2-engine mount), (2-bellhousing). Once those are threaded in by hand, lower it down and tighten them. Unless someone altered the frame, you have no trans mount, it's all engine and bellhousing and the trans floats.