This is a tough one. If I understand the TSB correctly, it's directing a valve cover change as being the solution to a condition that's chronically tripping the Malfunction Indicator Light. It isn't a recall, so it's not covered under those groundrules, and it is tripping the MIL light, so it is, effectively, and emissions control failure. Unless it's corrected you'd be unable to pass an emissions-required OBDII check, if your state requires such. Even if it doesn't, ignring the light would effectively render your "emissions system warning system (for lack of a better description)" unusable.
I think you have a good case here. I'd pursue it through the Ford chain of command defined in your owner's manual information. Keep copies of all the shop orders while you argue this.
Let us know how you make out.