I have built a “monopoly framed” or “chainsaw retrofit” roof (depending on which side of the border you are on), so I have a continuous WRB/air barrier from the first roof deck up the rake wall next to it. Now the roofers have put on their underlayment and step flashing on the second roof deck, which in my view is a secondary system mostly there to protect the primary barrier (VP100 blueskin). 

A layer of Rockwool and 3/4” rain-screen with siding will go over the step flashing, so most bulk water will roll down the CI, but if something does make it all the way to the back, should I worry about diverting it, that is tape the flashing so it goes onto the roof/ secondary deck.

Or is this a trivial concern, and taping it will guarantee that a future roof repair/replacement will destroy the primary WRB when the step flashing is ripped out.

I guess there is a third PITA option of cutting a long strip of flashing that goes over the step flashing, gets taped to the WRB, but is free so that the step flashing could be slid out and slid back in.