Tiny holes are very difficult to print to an exact size. Try pouring honey or yoghurt in an exact shape. Molten PLA is similar.
I think it would be best to post-process the model, and manually (!) drill the holes to the exact diameter. First print holes that are close enough, and then manually clean them up. I use a separate drill chuck for this: this gives a good grip and enough torque, and it allows a very slow and gentle drilling with good feeling, but without melting the material (which is a problem in electric drilling).
Small circular holes printed with most filaments (especially PLA) will come out smaller than designed, because the material pulls together before it cools. The degree of shrinkage will depend on the printer, the material, and the size and orientation of the holes.
You may find https://www.thingiverse.com/thing:2918438 to be useful in testing exactly how much larger the STL file's holes need to be in order to come out the right size.
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