The bellhousing-trans, and trans case bolts are more critical, since they're sealing oil in the trans, and holding the bearings, etc., in place. The tolerances are more critical there. The trans-engine bolts are not doing so critical a job. Lots of cars are running around with one or more upper engine-trans bolts missing, coarse nuts on fine studs, missing location dowels, etc., without too much damage.
The engine I just took out of a 73 Spider was missing both bellhousing locating dowels and was working fine.
Andrew