I’ve found the o-flute bits cut a bit narrower of a hole. if you edit the diameter you can correct it (no idea if this is encouraged behavior but I use those bits a lot)
The stepper motors are done in MM. If you are using inch then it is converted to metric under the covers. This has caused a few problems for people in the past. The other thing on an SO3 can be belt stretch. That is really not a big issue but can be a problem when trying to get really precise holes. What I suggest is you create a large square of a certain size the cut it. Then precisely measure it. If it is consistently too large or small then you can tweek the steps in the controller to get an exact size. This is not a very common issue but is possible. It is refered to as calibration.
One last thing to check is your HDZ lubrication. The HDZ goes up an down but it has to be oiled periodically. Not like to cause an X/Y problem but is necessary to maintain precision. The SO3 is belt drives on X and Y but is a very precise machine. One last thing to consider is your bit may not be the advertised size. Many 1/4" bits are really not 1/4". This will cause precision problems. So as others suggested just increase the size of the circle until you get the exact size hole you need.