I know what you mean but the pipe flanges do match the grooves in the mounting flanges. On the more straight ones all is pretty well flush. With the really warped one the original dimensions look like they match but nothing fits properly due to it being nowhere near flat.
New ones are the answer. Only issue is what colour to paint them: bright red to match the tubes and other engine details (push rod tubes, starter ring, rear accessory case, rocker covers), grey to match the main crankcase, or black to match the new cylinder barrels, mags etc.
Gotta love an engine that looks as cool as it runs.