While I generally agree with you, my approach is to avoid purchasing things that will have to go away in the future, or adding to systems that have been previously worked...
So from my perspective, the long tube headers are a small expense if done on the front end so that the exhaust part of the system is ready for whatever the future plans turn out to be. It is the same with the CAI in my mind...if you are ever going to consider forced induction the CAI would be a mod that would probably be a side step and would have to go away.
I guess the best guidance is to "begin with the end in mind."
If you know where you want to end up, the decisions in process are clear. If you don't know what you want as the final product, I opt for "never having to go back."