Just to clarify, you mean if Character A leveled from 1 to 20 as a monk, and character B leveled from 1 to 20 as a wizard, would the monk have an innately higher Hp (even after changing to another class) and the wizard have an innately higher MP and MATK (also after changing to another class), then yes.

Theres some FAQ I read where it explained what "Stat Gains" a character would get it he went from 1 to 99 on a single job. Monk would have gained an innate 250 or something Hp, and an insane amount of Phys Attack, etc. Let me see if i can go find it