Uneven flow distribution from the manifold, difference in flow in header primaries, difference in flow between injectors.

Also note the M90 pulses air into the LIM, look at the MAP in your logs, it jumps to say the least.

They're all going to be there one way or another. I can't see how a fraction of a CC of combustion chamber volume would affect anything.

If the internet is to believed, the dents will create hot spots, for more KR goodness.