You aren't missing anything. There is nothing wrong with PPP if you always remember what it is. PPP is tipoli and white diamond polishing compounds in a carrier of carnauba wax, and it leaves a coating of the carnauba wax on the wood. Being a wax, that means that it easy to apply, but the least durable finish we can put on a pen.
Will the PPP look like crap in a few months?? It won't take a few months unless you leave the pen in a drawer. The wax will wear off in a few days to a few weeks, depending on how much it is used and who is using it. When that happens, you are back to the bare wood. If the wood was highly polished before applying the wax, it will look good. If the wood looked like crap before using the PPP, it will return to looking like crap. If you had used a finish under the PPP, you will soon return to that finish.
CA glue is a plastic, and as such it feels and looks like a plastic. If you want a more "woody" look and feel, you will have to use a softer and less durable finish.