First and foremost - DO NOT OPERATE the boat with only one bolt in place. Structurally the hull, tower, and other pieces can take the load, but your safety factor drops considerably, and it's not worth the risk. We've had one member injured with a failed tower attachment in rough waters. Tower happens to land right around the back of your neck/shoulder interface when standing at the wheel.
Now, for the technical side. The thread on the bolt looks OK from here. That first thread isn't great, but I've seen worse bolts in other applications work acceptably. The insert in the base looks VERY torn up. Unsure if this was cross threaded, or otherwise damaged, however I would say that is the problem of the two. That is a stainless "thread in insert" in an aluminum block.
My first step would be to contact the dealer. This is 100% a warranty issue IMO, and I would be asking for a replacement mount and replacement tower hardware. My suspicion is that Yamaha will fight you on that, but it's hard to say for certain. It's the place to start though, as getting these replacement parts from the tower vendor is impossible (had a few members try). The towers are made by XTP, which is a subsidiary of Monster Tower, and they won't sell around Yamaha.
Second step if the dealer is of no help, would be to remove the hardware from the tower, and see if you can thread the bolt in WITHOUT the tower in place. This will tell you if the insert or bolt is damaged beyond repair. Once there, we can probably figure out a solution to repairing either. If available, you can run a tap through the insert, and a die over the bolt to attempt to repair the threads. Be careful with that, as removing too much material can lead to the bolted joint not locking properly, and this is a vibration prone joint.
