Many in this situation are filing/grinding down the carriage bolt heads to fit . . . not sure how extensive your toolshop is, but that is an option.
Grinding down the bolt cap is something I tried. The problem is that the square profile of the carriage bolt is too wide for the profile/track in the extrusion. The square part of the bolt is too small to grind down - there's no way I can reasonably do that, especially given that I need 16 such bolts for immediate use. The other option is to remove all cross bars and use a router or table saw to widen the interior profile/track, but I'm not about to do that for a product that should have worked from the get-go. Too much effort and I'm quite certain I won't be happy with the end result.