5mm which way?

If its nearside / offside, just position the brackets correctly. The brackets are much wider than the 25mm box so you'll be hanging out from the bracket anyway.

If you're really worried, weld an extra bit of box an inch either side of the bracket.

There's not much problem with the top brackets, which are welded to the bottom of the rails, but the bottom brackets are welded to the sides of rails. Hence TT's idea about pocketing the rails.