OK, so I went to change the front bolt out from a 6mm tinfoil bolt to a 5/16 Grade 8 bolt. I replaced the rear studs with Grade 5.5 metric bolts (metric all-thread's not available here)
After getting everything loose I found that since I took the front derailleur off I can get the motor to set down on the frame the "proper" way.
So no single bolt in the downtube, I have the saddle and clamp plate fastened down the "correct" way.