I just did this. I was intimidated at first, but researched a bit online and went for it.
I ordered the appropriate sized aluminum "brazier head" rivets off amazon. Might have to drill one out to make sure you get the right size before you order them.
Go to harbor freight and buy their cheap...
I recently bought a 1560 Jon boat with a completely rotted transom. What was left was literally dirt and completely rotted. The idiot hung a 9.9 mercury outboard off it, anyways. Incredible the thin aluminum managed, but not without some damage. Another story. Anyways, after much research...
Definitely not a deal killer. Very easy to fix leaky rivets by rebucking, as a few pointed out above. I bought a boat with a completely rotted transom. It had rotted and just about turned into dirt. Had to drill 8 rivets out and install new ones to fit the new transom. Harbor freight air...
After tons of research, I used 4200 on a 15' x 5' aluminum boat I just rebuilt so I could remove the bolts in the future if I ever needed to. Holding up great, zero leaks.