some of this has to do with how long ago the two species diverged. As far as I know, and unfortunately, no one is doing work on nep genetics. The crosses you mentioned that can't be done, well, my theory on those types of things is that those species diverged a loooooooong time ago. I haven't seen evidence for or against what I think (though I'm sure there is some...somewhere), but my hypothesis is that nepenthes experience an extremely slow rate of speciation. Competition is over a resource that is limited and limiting. In my mind, neps do not experience this very strongly. They need poor soil and sunlight to survive. The soil conditions where neps occur is neither limited or limiting, and sunlight barely classifies as either even in a strict sense. Another plant might whade the sun out, but isnt bright shade exactly what neps want? Also, you can "classify" neps into "families". In my head, I have the thorelii family, i.e. thorelii, smilesii, 'king tiger', 'giant tiger'....and the rajah family, i.e. rajah, mira, burbidgeae, etc. Without getting too much into genetics...morphology is NOT a good way to classify things. If we were back in the days of natural history, that would be all well and good, but these days you can't look at a pool of individuals and say, z.B.: "oh these 2 have big noses, so they must be related". Also when considering crosses, often times genes are not compatible with each other, no matter how similar they are. There is a figure in (I believe) Scientists Confront Creationism, that explains that cyctochrome-c differs within mammals by only a fraction of a percent. Also, we share what? 99% or something of our DNA with apes, yet a man/ape hybrid is not possible. In fact, our DNA differs with ducks by only 90something%, yet that hybrid isnt possible either. Until someone does a LOT of sequencing work with neps, we won't know exactly why certain hybrids aren't possible, or exactly what is more closely related to what, etc. Personally I don't believe anything I hear about CP evolutionary relationships until I see proof. What are you comparing? Morphology? That went out in the days of Linnaeus. Are you looking at the fossil record? Oh wait, there isn't one (with the exception of seeds of Aldrovanda). Answers to the questions you have will take a lot more time and a lot more research. Unfortunately for us, there aren't many people in the CP world compared to other fields, and for the ones that are, I'm sure its a tad difficult to get funding, as the people who give funding out have this notion that for research to be funded these days, it HAS to be profitable.
I hope that sort of...kind of...answered your questions