So, secret knowledge... I don't think I gained a whole lot of knowledge that I wouldn't have when reading the books in a logical order, but I made some connections that I think I wouldn't have made otherwise. For example in one of the Q Continuum books there's a war between (nigh-)omnipotent beings and someone throws an meteor at someone else and that's the meteor that crashes into Earth and kills off the dinosaurs, an event that James Kirk witnesses and even supports in First Frontier. It was kinda neat to see how these events flow into each-other back to back and not years apart from each-other.
I think the best part about my weird reading order is the 20th century. Watching the 20th century time travel episodes and reading the major novels in that time period (From History's Shadow, The Rise and Fall of Khan Noonien Singh Volume I Elusive Salvation and The Rise and Fall of Khan Noonien Singh Volume II) in the 100% correct timeline order is oddly satisfying and I'd actually recommend it. The novels and episodes all flow into each other and out of each other very seamlessly. Of course all these novels are very good in their own rights, but combining them with the episodes to one mega-story is an additional point of awesomeness.
Also, there are two Captain Proton adventures that I probably would have missed if it weren't for my weird reading order.
The 22nd century is a lot more boring; it's basically three flashback chapters from some books and then the normal Enterprise reading/watching order. The 23rd century is of course a chronological nightmare, but I think I've made senes of 2267 and 2268 now.