First off, I do not know where Gallatin or Hilham are so do not know what kind of fishing you plan to do so can not advise you about whether or not your Drifter kayak is well suited, but it is a fast and stable kayak. It is a wet kayak for a 300 pounder, but where I live (south Florida) that is not a problem 10 months of the year. The wet even feels good.
Air has to get in and out of sit on top kayaks. They go from being in the hot sun to being put into cold water and the air expands or contracts and has to go somewhere or the kayak will become deformed right from the git-go. In other words, they can not really be "sealed". I have six kayaks and a canoe and my 'favorite' kayak is a sit on top and it stays dry inside and I sometimes launch through the surf and even in a rain storm, the inside stays dry, but I did a few things to it so it stays that way. Even so, air has to be able to get in and out and (without seeing it) it sounds like air is getting out around a rod holder. It should be no big deal.
The only way to tell if there is a crack leaking water is to take your kayak into the water and looking inside after taking the kayak through it's paces. Most kayaks will end up with less than a cup of water inside if it is well put together (hey! there can even be condensation and the water can even be "distilled" and not salty while on the ocean). Cracks can easily be repaired too and some of them will only show up in use (water inside may not come out a crack when out of the water).
For now, and maybe always to be safe, store things that have to stay dry inside a baggie or some water proof bag while inside your hull. Stick a large sponge in there too (not in the baggie - in the hull). Enjoy your new kayak. I feel it will be just fine.
Organizer, Kayak Fishing Club of the Palm Beaches
West Palm Beach, Florida