Those dumps won't hurt anything. I've seen crappier manifolds with sharper and shorter re-entries on a B-series motor (your comparison) breaking 400 by 15-16 psi.
What are you tuning it on? And, my experience with stock cam RB25's is they continue to pull harder and harder especially past 6K. Your dyno sheet's smoothing is on 5, and past 6K the power output levels off and gets all sorts of lumpy. I see that on other motors when the cam timing is not ideal, or you might have a boost leak manifesting ie - BOV coming open, coupler allowing boost to leak off between itself and the charge piping, etc.
Yeah on lower boost peak power comes at redline (7500) and the power curve looks normal, however the more boost the more the horsepower levels off it seems... when i built the downpipe, and recicred the wastegates i didnt really think it would hinder it much, but ive heard both sides of the fence on the issue.. it seems like a restriction to me just because of how the power levels off on higher boost and the compressor having alot left in it. ( i know i forgot to mention that in the OP)
I need to change the wg springs, boost wouldnt hold anything above 20psi it would spike to 25-26psi and fall, i was having some breakup on higher boost but increasing the dwell pretty much eliminated it... maybe its was missing ever so slightly??
You think cam timing could be off a tooth? i wondered this myslef, but i thought it would have a much larger effect...
Im running a New Haltech platinum pro its a fairly new unit, seems pretty soild to me, Dave liked it too