I regularly work with cut to size parts because I put them in a vise. It is much faster to cut parts to size on a table saw/radial arm saw. Just finished up all the blocks for a Foredom bit/tools case I am building, IIRC there are 22 blocks in the case, half of them have pockets in them. The rest have various size holes for the bits.
When I do NOT use cut to size parts is when the piece needs radiused corners. Well, sometimes I will put them on using the disc sander. . . . but only small ones.
This sounds like a setting XY zero problem.
I use a .5 sq aluminum bar to do it. Put a .5 dowel pin in the collet. Then bump the dowel pin up against the .5 "feeler" gage. If I am on the lower left and doing X then I enter -.75 into the DRO. Y is -.75. Where does the .75 come from? The half inch bar and half of the dowel pin.
Low Profile CNC Router Vise