Do your best!

I have seen the front bolts (2 on either side at front of heater channels) turn out pretty rough. The two under the gas tank are usually decent, the ones in the heater channels are hit or miss. The ones on the back cross rail (in front of the torsion housing) are pretty straight forward. The rear body mounts are the bigger ones and can be a booger but not awful. If they look crusty, they will be tough.

Be careful forcing anything because if the bolt is rusted in place, chances are that "place" will spin out with the bolt.

I think as long as you seal up the gap with a new seal and get most of the bolts in, it'll be fine for a rat rod.

Is the body a total loss or is there something I can do?

After seeing what Rick did converting a pile of rust back into a double cab truck, NOTHING is a total loss.  There are panels avalible for repairing almost every part of a Beetle body.