I know it isn't the regular way of doing things
All the bolts are definitely 90° to the back of the transom. As the motor is mounted at the height of being one hole up whilst using the top holes the bolt heads on the inside are pretty much at the edge of the full thickness lower part of the transom. You can see the washers are bent over the edge.
I'm just worried that if I were to just remove the extra set of bolts to raise the engine a hole them being so close to the top of the transom may lead to problems.
I think they probably just drilled the top holes a little high and then decided to put two more bolts in the bottom as a "quick fix".