Matt Wilson

Here's a possibility.  I wonder if the Dodge rod bolts have threads that are cut, while the Pontiac rod bolts have rolled threads.  Rolled threads are formed by dies that displace (smash) the material into the shape of threads, without removing any material.  This results in threads that have larger outside diameter than the adjacent shank section of the bolt.  On the other hand, cut threads are just that - they are made by cutting material away to achieve the thread shape, so the threaded section diameter will not be any larger than the diameter of the adjacent shank.  It's kind of hard to tell from your photo, but it looks like that might be the situation.  If so, then accordingly, the Dodge rod might be made with smaller bolt holes to snugly fit its cut-thread bolts, but the Pontiac bolts, with their rolled threads are too large to fit.
 
I have a couple of Dodge 230 flathead rods at home, along with their bolts, and I can tell you that the threads in those bolts have the appearance of being cut, which surprised me, since I have seen  other Dodge flatheads that have the appearance of having rolled threads.  I have no reason to think that those are not the original bolts, and perhaps they were early rods that used cut-thread bolts.  I could take some measurements and photos of those rods and bolts some time in the next few days and we can see if they match the dimensions of your bolts.  We can also see how thin my other rods are (the ones that used rolled-thread bolts) in the wall between the bolt holes and the bearing saddles.  I remember them being pretty thin.  We might find that you have room to ream out the bolt holes in your rods to accommodate the slightly larger Pontiac bolts, or some aftermarket bolts, such as those from ARP.
 
From the strength and durability (fatigue) standpoint, the bolts containing rolled threads are very much preferred.  I believe virtually every manufacturer uses those types of rod bolts nowadays and have for many, many decades.  I remember seeing early rod bolts from other engine makes that used cut-thread bolts, but I think most everyone moved away from that type of design long ago.

Many aftermarket bearings have been made that way, but it's not correct.  It will restrict oil flow to the bearing.  You'll need to take a file or Dremel tool with appropriate attachment and open up the hole in the bearing to match the oblong shape of the hole in the engine block.