I spent a lot of the last three or four years getting handed all kinds of different random pistols to shoot and evaluate and they all came with different random sights so I feel like I've got five hundred rounds on every sight combination known to man.
I have been using sharpie'd rear three dots on most of my personal guns for as long as I can remember. Maybe fifteen years? So part of my bias towards that arrangement is just familiarity. But I think traditional 3-dots with dimmed rears are awesome. I do also like some of the bar-dot sights and other oddball combos but for me the 3-dots work really well.
I have never once been confused about which was the front. That's down to body index. I have done plenty of low-light stuff, including a LL module with Ken Hackathorn and several low-light specific, multi-day classes. I know other people have done more, I'm not trying to make a claim that I'm a particular expert in the area, I'm just saying that I think if there was a situation where my gear would surprise me, I'd have stumbled across it by now. 3 dots work well for me.
I had the same problem when I purchased my 3913 TSW. I was shooting low. I called Smith and the rep sent me another Novak sight. When I called them back the lady I spoke with immediately asked about my sight picture. Between flinch and sight picture over the years I've been able to correct the issue.