I have a second option, which is to put a 3mm strip of metal between the frame and the 12mm threaded rod, thus aligning it with the holes in the hardox..... sounds like it might be the easier choice. The hardox has other points of attachment that don't have any issues, so I think this would be an ok fix :x
Good advice though, I have plenty of cutting oil, might need a higher quality drillbit though if I do try to drill it!