I see what you're talking about. I don't know how you have the top lined up on the rim's when you took the photo. You will line up the top (and back for that matter), so that the center SEAM of the top, where it was glued together, is lined up on the
center of the neck and tail blocks.I always glue the back onto the rim's, then the top, so I don't have a photo of how it looks when the top is centered, but I do have photos of the back on center. I know the back center seam is covered by the reinforcing strip, so you can't see the actual seam, but that seam is what is put on center of the neck and tail blocks, on both the top and back. This is why we make the top and back oversized, so we have some wiggle room to ensure that these seams are what are centered on the blocks themselves, not necessarily where the rim's meet on the neck and tail blocks.
If your transverse brace is off center a little, and you're worried about that hole not lining up with the hole for your truss rod in the neck, there shouldn't be a problem. If you stick a 4mm Allen wrench through that hole, which is what it's there for, you'll find you can move the wrench around to engage the rod. That hole would have to way way off to give you any problems.
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