Cullen,
Yes, when I do the front side and set the zero to the middle of the piece, then it doesn’t matter if you have a slight difference in size on each side. To start, I mark the edge that will be against the fence and it will be the only part that touches it. If my material is perfect, I could pick any spot and as long as I repeat it on the back and there is enough material, it will work. In my case, a 38" x 6"x .8" board for a bass guitar neck. It was not exactly 38", so I just measured 19" from a side(left side) and made the vertical mark. It was exactly 6", so I made the horizontal at 3". Where they crossed, I used a sharp VBit to get exactly on it. Remember which sides you made the measurements from.
I do the whole front side, 6 toolpaths with various bits. In my case, I then flip Left to Right keeping the original side against the fence. I bring the spindle to Current XY. Now remembering which side you made the measurements from, for me 3" from the fence and 19" from now, what is the right side of the material( I measured from the left to start), I make the lines. Only bring the Z down, do not change the XY! Your fence is not moving, so you can slide the material right under the bit. Once it is there, use your clamps to lock it down. Start your job.
For using dowel pins, you would put them on the centerline of the X in my case. Your XY Zero needs to be exactly in the middle. Since I knew my material was not perfect, slight angle at the end, I did not use them. With the fence and the material same side against it, you only have to slide it left and right to get the same perfect center. I did a double check by taking the line from the front and extending it all the way around when I first set it up. With a 60 degree Vbit, it locks right on the 0.5mm pencil lead perfectly! Cut the back with 4 more tool paths and was good to go.
Full disclosure, I screwed up about 15 of these attempts until I realized that two sided cuts, or 3D cuts, will never work right from the lower left corner, or any corner. Left Center would work if you have a Y axis fence. You just always need to have the center on the midline of your model and material. I also tested BitZero, and it is accurate and repeatable, if your material is accurate. If the two corners are not equidistant from absolute center, you will have offset.
Let me know if this makes sense.