And your mortise would be too small. Because it’s not removing as much material as it thinks it is.
I haven’t made any mortise and tenons with my machine, but I made some finger joints (or box joints) on the edge of a ply to make a 3 sided box. I can’t find the file right now though, so I couldn’t tell you if I added any tolerance, but if I was to make it today, I would add some, so I probably did… Not very confident though. Box joints aren’t affected by material thickness either.