Does the reduced thread size bother you?
Not particularly, since the shank is carrying the shear load. Most of the crossmember rivets are 1/4" diameter, so reaming up to a 3/8" shoulder to eliminate any egg shape in the hole is increasing the shear area by 50%, and the 5/16" thread should be plenty strong since all it's doing is holding the bolt into the hole. The whole works is bigger and stronger than the original fastener. The whole idea of riveting is to eliminate ALL the possibility of movement between the parts by filling the entire hole. A reamed hole and a tight-fitting shoulder bolt is the next best thing.
Jerry