The size needed for the hole is something along a formula of:
bolt nominal size
+
bolt tolerance
+
hole size manufacturing tolerance
+
in case of multiple holes, the manufacturing tolerance for the location of the holes, times two
+
hole manufacturing tolerance for the other piece its going to be mounted to
+
again, in case of multiple mounting holes, the manufacturing tolerance for the location of the holes, for the other piece, times two.
Looking this up from a table is a total and complete fallacy, even though commonplace; it show's the people are not using their brain at all. These tables do exist for a reason: they are pre-calculated tables to speed up workers but are always specific to certain processes and products. For your project, they are completely random numbers and bear no meaning whatsoever.
An example:
You have a PCB manufactured with mounting holes for M4 screws. The manufacturing tolerance for the PCB holes is something like +/-0.05mm, for both location and size. M4 screw is never over 4mm. If you mount two such similar boards together, you'll get away with something like 4.3mm holes (4 + 0.05 + 2*0.05 + 0.05 + 2*0.05), despite any table saying you "need" 4.5mm or so. Your tolerances are good.
Now, if you screw said PCB to a case, but for prototyping, need to hand-drill the mounting holes, and you are only able to locate the holes +/-1mm. Now your holes need to be extra wiggly, because imagine one tapped mounting hole of the case 1mm to the left. Now the mounting hole on the PCB needs to have 1mm excess in all directions - meaning 2mm bigger diameter. So, you need 6mm holes, even though you'll find a table saying 4.5mm is enough.
In some cases, you need to take the different thermal expansion coeffs into account, and the formula can get really fancy. And I'm not even sure if it's exactly correct. I haven't looked this up from anywhere. This is simple mechanical stuff, use your brain.
Note that the precalculated "rule of thumb" tables are originating from machine shops. They tend to have fairly good tools and experienced staff, but OTOH don't tend to have the latest CNC hightech (especially since the tables floating around are ages old). This means, the tables are a bit pessimistic for a modern CNC stuff, leaving more margin than you actually need; and they are optimistic for a hobbyist or unexperienced worker working with manual tools, resulting in holes too tight, and things won't fit without extra filing.