This is working as intended
I don't buy it.

Seems more like an OVERSIGHT to me.

In their very sad attempt to having some kind of character customization and old-school rpg element, SE added stat points. Of course, there is basically only one viable choice for each job. Then later they and people realized it had the side effect of screwing over Scholar/Summoner if you want to play both, and now they need to think of a way to fix it or are too lazy to.

People saying other class/job combos will have this problem---not necessarily. The reason Arcanist jobs have this problem is because it's a DPS changing to a healer and vise versa. Will a pugilist have this problem when they add another job for that class? Probably not. Will a thaumaturge have that problem? Probably not.

The game is full of conflicts like this and they are directly opposed to the goal of the class system in the first place: that you can play what you want when you want. PvP is getting boned the absolute hardest at the moment to where you can only viably play one class/job.