I'm with Kevin on the easy fix of cutting off enough of the bolt head to allow it to fit beside that piece of metal.
I would then weld the head of that bolt to the that piece of metal to keep it in place. I would put the motor mount in place and tighten up the nuts before welding to ensure that the bolts a aligned.
I believe that the original carriage bolts were welded a tiny little bit on the assembly line which did not hold up very well.
The problem that occurs over time is that the rubber deteriorates, causing the nuts to no longer be tight, causing stress on the square holes and they wallow out round preventing the square carriage bolt to hold while trying to loosen the nuts once rust locks them to the bolts.
