There are many questions that need to be answered but at the time all we can do is just wait. Your question regarding leveling up the class to maximum and having an issue as the job would be automatically leveled is but one. Another one is, what if you level up SCH up to 50, do you automatically have SMN to 50 as well?

We've been brought up in the old 1.xx way of thinking that 1 class = 1 job so naturally these questions do come up in that vein. BUT, at current we can only access classes in the beta. It is possible that Yoshi has done that for a specific reason. Rumor has it that the sub-classes for each specific jobs have been reworked. Take that for what you will, I'm just stating that it's a possibility of something else.