ringman,
If I am specifying holes for screws and bolts, the error that will get me in trouble is a radial deviation from nominal. My optimal tolerance zone is circular. A rectangular tolerance zone that accomplishes the same thing will have a much smaller area, and it will reject parts that will work.
If you are fabricating one set of holes and using these to pilot the mating holes, then mating the bolts does not matter. The next requirement is the location of your bolts.
Is there anything the bolts might interfere with?
How much like a piece of crap is it acceptable for your assembly to look like?
I think your tolerance zones still should be circular, but it really depends on your requirements.
JHG