I've sometimes wondered if this misalignement could be caused by very slight fork leg misalignment. The main downside of this is fork stiction, but perhaps this could result in a fender slightly askew. Slight axial distortion or lateral offset could cause the wheel to point slightly off-center.
Apologies if this is well known to you and this is the procedure you follow (since this is by-the-book for just about any bike), but there are some key steps to perform when installing the front wheel to achieve fork alignment and minimize stiction. I underlined the ones that I could imagine people skipping. From the Honda service manual.
Anyway - maybe worth checking? Just kind of a guess on my part.