Will a 6mm dowel fit in this hole?

Hi! Yes, knowing the tolerances of FDM your best best is to slightly oversize the hole. E.g., offset the face by 0.13 mm (which will open the hole up by 0.26 mm overall) for a tight fit, or 0.18 mm if a small air gap is OK. I also recommend using solid infill as it makes it easier in using a drill or reamer to hit a desired size post printing (this can easily be done with a hand drill or press).

Now, looking at your file I do have to ask if you’ve considered SLS or MJF? Those little side holes are for a set screw, right? In FDM they’ll look oblong and coarse. SLS and MJF post-drill like butter so you can build the part and drill/ream to your precision needs.