Confirmed, sort of.
Both the WS Self TP power and the PB Energy flight appear on the list when the level 1 power is chosen. When the level 2 power is taken, Ninja Run appears in their place, but only in Dynamic Mode.
In Level up Mode, the inherent never appears, or vanished too quickly to be noticed.
I also made a history print out of a PB with random powers chosen to level 41 (Dynamic with no slots). Energy flight does not show up on that print out, but Ninja Run is listed as being granted at level 44.*
I loaded a completed build and Energy Flight was missing from the screen display, and both printouts, but Ninja Run was back at level 2.
For PB and WS, in either Level up, or Dynamic mode, the level indicator on Ninja Run will advance to be the next power taken every time a power is selected. As you take the level 4 power, it becomes the level 6 one. When you take something at 6, NR moves to 8. It doesn't do this for other AT's.
Also, NR isn't available in game at level 2, but all AT's have it listed that way.
Happy Hunting