Barry.  I don’t use that particular bellhousing bolt on the FE to Y-Block conversion.  I’ve deemed the countersunk allen-head bolt used to fasten the adapter to the back of the block of higher importance than having that particular bolt in place.  At this point, the five bolts on the bellhousing is sufficient as the majority of any twist at the bellhousing puts stress on the two ½” dowels that actually aligns the bellhousing.  I’ll add that when mating the PG tranny to the FE in the conventional manner, the same issue arises and that particular bolt is not used at the block.  As Charlie mentions, rotating the transmission is also another option.  I did that on the Roadster with the PG tranny to Y conversion by clocking the transmission in a clockwise fashion looking from the back.  Just made sense if I was going to reclock the tranny to put the shift lever on the high side rather than force an oil leak from that point.

Mike's suggestion on plugging the hole and redrilling is also a good one.  In my case, the car can be swapped back and forth from a Y to a FE so that option is not viable without a second bellhousing.  But nothing says the hole can't be slotted in the mill and then using a stud with an appropriate washer over the slotted hole.