I hang around various forums and read the drive train stuff. There was a real rash of chain to big ring rub, like yours, right after Shimano made some "upgrades" to their 9-speed Ultegra cranks a few years ago. I think they may have a slight design flaw or quality control problem because it seems to be common with many (not all) Ultegra doubles while the rest of the 9-speed cranks don't have this particular problem. The BB spacer (usually 2mm) is the normal cure, and it works well.
I would not fully cross chain to small-small, but I think you should be able to occasionally use the second and third smallest cogs with your inside chainring.

Al