I’m not sure I understand your question. Do the A and B and C settings as you term them refer to the three mortise width settings?
On my 500, the three width setting cut narrow, wide, and wider mortises, but the tenon fits snugly into all three the same. The depth and height of the mortise stay the same while the width varies.
I normally will cut all narrow mortises in one board and the medium mortise across the other board. This allows me a tiny, but usually sufficient, adjustment room upon glue up. I can tap the boards into perfect alignment.
Using all narrow mortises in both boards would require extreme precision. One would need perfect placement of all mortises to get the boards to go together.
Now, if the three settings produce mortises of different height where the tenon isn’t a snug fit, that sounds like a Festool Service problem.