From an engineering point of view it only makes sense to add some non-zero tolerance. Even when machining on our large CNC mills on my work, we always add a bit of clearance denpending on material, mill, etc. You never design a part to fit perfectly with no tolerance within another part.
Obviously it is difficult/impossible to add something matching everyone’s 3D printer, but that’s not really the problem here. The issue is that the rest of the parts (at least the ones I have printed) have added tolerances, but this single part does not. Again: For me it’s not a problem, but I guess that if you have printed the first parts and they fit tightly, this this one will definitely not fit without some sanding/drilling.
FWIW I really think this project is awesome! 🙂 I am just pointing out that to me it was strange to see different tolerances and I honestly thought it was just a minor design flaw.