Is that really the "Lego" plastic building blocks sold as kids' toys, or is "Lego" a slang term for a mounting scheme with a similar appearance but a different formal name?
I don't have direct, personal, experience with your question on hole sizes and tolerances. A few incarnations ago the place I worked had a board on which they imposed some tighter-than-normal dimensional tolerances. It was sometimes mentioned as an example of something that design engineers should NOT do to ensure company profitability, employee bonuses, etc. I got the impression that pretty much any shape, with any tolerance, was possible . . . for a price.
I think that's a valid concern. Where I'm working now, we see tool wear problems on carbide router bits and we're cutting HDPE polyethylene. I imagine that a drill bit used on FR-4 fiberglass will make measurably different hole sizes across its service lifetime. You may end up calling out a specific hole size, and tolerance, on your drawing or purchase order and paying a surcharge for the vendor to comply with the requirement.
Or, like @Joan_Sparky suggested, the best approach in the long run may be to call out an undersized hole and finish it to size locally. This might be done by your own company, or jobbed out to a machine shop. And, it may be better to call out a significantly undersized hole - say, 5.5mm or 6mm - so the final drill or reamer can get a good "bite" in the material rather than simply deforming its way through the pilot hole.
What are the actual requirements of the mated holes and studs - an easy assembly fit, a close (no play) fit, or snug (locked in place) joint? Does the hole diameter have to be sufficiently oversize to absorb locational tolerances? Do you have a good idea of what the usable hole dimensions are? I'd guess that Lego blocks go together so well at least partly due to the draft (taper) forced onto the mating studs and sockets by the casting molds. Getting a snug fit on tapered surfaces is MUCH easier than machining a line-on-line fit with straight surfaces. The tapered reamer idea may be a good choice!