"A wizard should know better", or as I like to say, "Don't do that..."
On a slightly more serious note, this seems to be one flaw in the uniqueness logic which is used to calculate the "difference" between the Rune Priests, thus if you take identical Rune Priests with the same psychic powers, but change one of the the bolt pistols to a plasma pistol they are no longer identical. This is because the built in functions of AB are looking at the big picture and not "sections" of that big picture (e.g., wargear duplicates, psychic power duplicates, etc.). So ideally it should be looking at the psychic powers, see the duplication and flag it, and will constantly fail uniqueness even if you would try to change the wargear.
I'm not quite sure if LW can offer a suggestion for this as I think it would require a separation of the Combo logic to have separate groupings - Combos1, Combos2, etc. but still have the ability to see all of the combo categories as a whole. I'm also wondering about using tags and traditional scripting to at least solve this one problem.
For the short term, I'm not quite sure of any other workaround apart from 1) read your codex, and 2) always carry around the hardback rulebook to slap anyone who didn't read their codex...
(its more like I have had a long busy few weeks)