Depends what equipment and facilities you have access to. The gearbox move lying on your back rolling about on the ground sure seems like a pain when you could lift the engine out and 95% of the work can be done from above.
When I did my 2.5NA I did both, when I took the gearbox out I had a 4 post and was semi sheltered even at that it was not easy to manhandle a complete gearbox/transfer box assembly about, the second time I took the engine out, lifted it right out, lots of light and space and it was a breeze.
I recently put a new gearbox into my 90 and I did it outside, but this time I took the seatbox out, I was then able to stand over the boxes and just lift them out; extra hands are useful if you can get them and save having to rig up lifting gear, had I not had people about I would have done the seatbox method and used a engine crane through the door. I went for this option because it was -7 out, ice on the ground and I didn't fancy rolling about on my back too much.