The starter bolts to the trans, the lower right hole is for the bellhousing and take a larger bolt then the 3/8 bolts around the housing. I have seen many of the bolt holes broken off right where you are speaking of. Usually they get broke while on the engine stand. When a person is mounting the block to the stand. If half of the bolt hole is still there, many people just put a flat washer on the bolt and use it the existing way. The threads are in the bellhousing