tl;dr: Pillars have high accuracy compared to holes, so you don’t have to design around them. In terms of tolerances, you’ll mostly deal with filament and machine tolerances, which is +-.03mm in our case.
After our “How to design Holes” in 3D Printing guide, we decided to look at designing pillars, since they’re essentially the same problem, right?
We’re not sure why, but holes do not seem to be as precise as pillars even though the underlying physics is the same (one side connected to the piece, another not). I think it might be because of the slicer or the way the triangles in our STL files are generated. We’ll look into it more soon, but because many of our clients were asking for design considerations for pressure fits, we had to make some tests. When we printed out our pillars, they were all just like we designed, only +- .03mm from our specs.
If you’re looking for a test for your own printers, you can obtain the stl files we used here. He spaced them out just enough so a caliper can fit in between.