Honestly, I personally have this policy on PCM updates. If you're happy with how it runs, don't let them update anything.I don't let them touch the alignment unless there is a reason to, like irregular tire wear, darting to one side then the other, replacing tie rods, etc. My experience is 50/50 whether they improve alignment or screw something up. Sad to say, but I have the stories.
It's nearly impossible to avoid it, though, unless you avoid the dealer. If they plug in a dealer-level scan tool, odds are they'll flash any updates as SOP.
Exceptions might be updates that truly have a good chance of increasing engine or transmission life. ~15 years ago this would sound absurd but now manufacturers have convinced themselves they can fix faulty hard parts with software updates.