The way I read Fria's statement, only the frame rails on cars with 14" tires were modified - to avoid rubbing in a sharp left turn. 13" tires wouldn't have been a problem because that's what was used on the Falcon without issues..
Fria's book details the design and building of the very early Mustangs. When he talks about the practice of "using a torch to crudely cut away a portion of the outer lower lip of the rail", I believe he is talking about the 64-1/2 model year. Then when he is talking about the practice being "used into the next model year", I believe he is talking about '65.