It's not too difficult to balance.

If RDM is introduced, and has pre-reqs for both CNJ and THM 30 (or 20), when you unlock the Job you can apply the Job stone to it on both classes. It's spell arsenal consists of both THM and CNJ spells (up to level 30) and unique spells post-30. Thus it doesn't matter which class you use to switch into it, as it's essentially the same Job on both. Similarly, the EXP you obtain goes into the Class that you used to switch into RDM.

If there's more pre-reqs aside from CNJ and THM, they can be "second-tier" classes that can not change into the Job, but are required to obtain some proficiency in, say, sword and shield.

Then, each Class has a Job that is unique to it and a Job that is shared between two(or more) Classes.

Examples: MRD+LNC=>SAM. PGL+GLA=>THF/NIN. CNJ+THM=>RDM. ARC+"beastmaster"=>RNG(traps).