I think a good approach might be:

Has it been engineered?
Check with the engineer.

Who designed it?
Check with the designer.

Who is paying for it?
Check with person writing the check(s).

Is it green oak?
You'll likely see another 1/8" or more in shrinkage!

But overall, yes, you can vary things when the chisel meets wood. Unless that 1/4" +/- is critical and will hold up the entire building, it is probably fine. On a brace, I'd let the error be on the up / top side so as to not mess with the bearing surface, which is what should be critical for pushing against another timber.