So, i was happily cruising along in my mission and encountered a npc cruiser, fine i tought lets be clever and target its shield first.
Lo and behold its shield facing went down and he poped his metaphasic shield. And the shield facing was still down, but no damage was delivered.
To me thats pretty buggy.
If a shield facing is down, metaaphasic shielding should not work on that facing.
I agree with your explanation of what should happen.
I believe that what actually does happen in game is that while Metaphasic Shield is running the NPC ship (and its shields) becomes immune to all damage. Which means that they'd probably have to completely rebuild the power in order to get it to work the way you've described.
What are the chances of that happening? Heck, we can't even get them to fix the NPC Dual Pistol Bolt Spray bug!
Well, they could simply remove that shielding altogether.
Because its only a nuisance in the first place and giving something like that to a standard run of the mill npc but not a player is also wrong.