The overall quality of workmanship on the assembly appears excellent. I see no gaps between sheets, the rivet shop heads are set consistently and I observe no smilies occurring at or on any of the rivet manufactured heads. All these things suggest the builder was thoughtful and strove to produce a high quality airframe. You have every reason to believe the bolts are installed correctly too. In fact, I am heartened the builder repaired the "non-conformance" as well as he did. You can be sure other less thoughtful builders would have gone ahead and shot solid rivets into poorly prepared holes in keeping with that famous "Build on!" attitude. As an example, recently Van's suggested a builder actually install blind rivets into an elevator hinge bracket, a repair fix I consider dicey in this particular application because too many things can go wrong if the fasteners are installed incorrectly and that is all too easy to do for a brand new builder who doesn't have the experience, training or tools needed to correctly install structural blind rivets.
In your case, the bolt heads appear to lay flat (suggesting straight holes) and the thread protrusion is quite acceptable. Because the builder has demonstrated above average sheet metal skills, I would consider those bolts a worthy repair, no more than an additional detail to examine at condition inspection time and just leave it go at that.