Having read the article from KAR, I can only believe that it would be easier to do that job with the engine out of the way. The point that they get the engine to, would only require the removal of the starter( 2-3 bolts), the torque convertor cover and nuts(3 bolts and 4 nuts), mount bolts(2 or 4 depending on if you remove the mounts from the body or engine),and bell housing bolts(6 bolts). Since they have removed many engine parts while the engine was in, they could be taken off while the engine was out easier, as you would not have to bend over the body to reach them. It appears that the only thing they leave in is the brake MC and lines, and engine block. With the engine out of the way, it may make cleaning and painting easier, as you have more room to work.
I frankly don't see where the additional 12 hours they quote comes from. Since I have pulled small blocks out of Mustangs in less than 1 hour by myself, once the hood is off, and radiator is out. Also I would think they could do the compartment in less than 50 hours if the engine is out, instead of in their way.