I just hope they don't vandalize the exteriors any more than they already have.
But it would. Most of the EMD Tier whatever compliant rebuilds I have been seeing pictures of involve major modifications to the radiator section, and sometimes also dynamic brakes, air intakes, filter sections, overall roof height, hood end, and cab design. The 710 engines which are the most likely selection require much greater cooling capacity than the 645 for comparable horsepower (the 16 cylinder 645 would be replaced with a 10 or 12 cylinder 710). There's no way they will run an HEP alternator off the new prime mover, so they would have to find space somewhere for a genset and related carbody modifications. I think the F40Cs actually have some dead space and everything is shifted slightly forward relative to a typical SD40, but VIA used the back porch for the genset on their F40PH rebuilds. The F40Cs are different enough from both SD40s and F40PHs that their rebuild would be a custom design for only two locomotives, as far as how they get things to fit. Losing the chrome sides- it could happen.
As for the F40PHs that have just been rebuilt, I don't see them going through another rebuild. Metra itself is claiming that buying new locomotives is more cost effective than rebuilds, and there will be a whole new round of technology and regulations by that time anyway.