I have the factory traveler for my Wave. It's installed with rivets that came with the kit. You can mount it with screws if you needed to and you dont have to go through the entire cross bar. It would take some effort to attach the nuts. What I have done to attach nuts deep into places was to fashion an extension for my wrench. I have used a swifter pole and smashed the end around the wrench, (1/4" drive or box wrench) and with some patience, a flashlight and a helper I got the job done.
Now, on the Wave the cross bar end caps are held on by rivets, so the hulls would need to be removed from the cross bar and the rivets drilled (and replaced). With that said, it would be much easier to use rivets to attach the track no matter what brand you use.
You should be able to use countersunk rivets for the harken track