Think about it this way. You can unbolt and drop a manual transmission from under the truck easy enough. Not so with the H-M if it was designed to go in the same way. So, they designed it so that the engine could be removed leaving the trans in the truck and then dropping the trans from underneath. Or they made a tool to hook on the frame rails to support the rear of the engine and the trans could be removed while leaving engine in. To accomplish that, they needed access to the "bellhousing bolts" which is why the transmission cover is different. Then, there needs to be a provision to drop the transmission which is why the made bolt in crossmembers that can come out with the transmission or just be dropped to be out of the way. Same reason fro the brake line re-routing. It was all done in the name of serviceability.
