Concur with this. I have mostly gotten used to it, but did get frustrated the first few dozen times I tried to build flight plans and entered a VOR or other non-airport fix, and the iFly came up empty. Then remembered, "Oh yeah, gotta select the other stuff to search on", and re-did it. That's a far bigger waste of time than the extra few seconds the iFly might take to just search a larger database the first time.
Even though I'm used to the process, it's still annoying to have to go check some extra boxes for some waypoints I want to enter. I sure wish I could set a preference to make those selections persistent.