Safetypee, good points. Noted that the 146 a/p and f/d are completely separate systems and often don't agree.
The reason I mentioned it is because it was something I had particularly noticed as a difference between the two aircraft. The Dash 8 classic autopilot will put the cross hairs squarely in the middle of the box, "in the cats bum" as we'd say. In fact, it's been a while, but I seem to recall the Dash 8 flight director will "snap" to the centre of the box when you engage the autopilot, they will then move as a single unit. I don't know if the -400 is like this or not as I haven't flown it, but surely the op has observed these things.
The 146, when flying a steady attitude (i.e., not trying to manoeuvre), will always have the cross hairs aligned with the top of the box. I only suggest that looking at where the autopilot puts the box reference the flight director in steady flight on the Dash 8 400 would give a clue as to the intended pitch reference. This is all if it doesn't explicitly state the reference in the FCOM.
Personally I think the difference between flying the centre of the box vs the top is so small that it doesn't matter, but it obviously matters to someone.