Ishpurim: To be very fair, JTS had much greater rebbeim than YU, such as Geonim Saul Lieberman. And is certainly on par and in the same category of Yeshiva like YU.
And as you pointed out, Hebrew National is a world recognized hechsher. So to be fair to RM, his comment that “YU is to yeshivas as Hebrew National is to Kashrus” is a fair statement. Both YU and Hebrew National are choshuv establishments.