it's a good question
I'm building a non prepunched 6A, so can only speak from that experience (where everything on the plans are dimensioned).
You will have to use your judgment. Some dimensions are mandatory for strength, such as edge distances (with very occasional exceptions). Some are mandatory for fit, such as the location and alignment of stabilizer and elevator brackets and rod ends, or the reinforcing angles on the front stabilizer spars, which if made oversize won't fit, and if undersize, won't allow proper edge distance on the attach bolts through the longerons. For these types of things, my "tolerance" is to make the part as close to specification as can be achieved.
Other dimensions are more tolerant of variance. Where the lightening holes go in the battery box, or how large they are, is an obvious example where the builder has lots of discretion.
For the airframe construction, I have found that following the plans as exactly as I can has served me in good stead.
When you get to systems, including firewall penetrations, etc., you will find a lot more room, and perhaps need, for variance.
I am not sure what bracket came out .020 undersize, but if it fits, if edge distances can all be maintained, in other words, if it is functional and meets accepted aircraft construction techniques, I would think it is a good aircraft part.
Bill Brooks
Ottawa, Canada
RV-6A finishing kit