From the looks of the pick, the runner that hits the LIM is stopping the manifold from seating to the block all the way.
Have to play around with it, you can probably grind enough off the LIM to make it go on, take a little from here, little from there etc.
I'd think it would be OK as long as it doesn't touch and you're using some wrap or shields.
Decent manifold though
Worst case (and assuming there's room between the turbo/manifold and frame) is to space it out with another flange, or 3 12A individual flanges.