We did have a small number of large frames arrive (1 1/8″ steerer Soul2 type) a few years back with tubes welded on too low. I had them lab tested and they were fine so rather than waste all that effort and energy spent on making them by scrapping them we sold them off for 25% off with full warranty and full disclosure. Nothing shady going on there.
Moving on to the problem above, this is the first instance of this problem we’ve heard of on the Soul3, and we have those exact forks on demo bikes ourselves. Is it a small or XS frame? That is the worst case for clearance, but I am surprised as I have the crown drawings for most forks to check that kind of thing when I’m designing. Give us a shout with the full low down and we’ll figure something out.