I thought the same myself. What use for Party-Formation, if your Main-Character isn't an Meele fighter on the Front. Than again i thought, however, if they would implement it that way, that your Party takes Formation ones the fight beginns, it wouldn't be that dynamic anymore and would forgive to much, like if you mindlessly run into enemys/fight/ambush with your Mage or such.... I don't know an proper solution, maybe for Explorer-Mode?
Your first instinct was right. Your second thought was wrong.
Literally the only point of formations is to arrange your party on combat. If it doesn't do that, it's not working. If your formation has the mages at the back properly, but they are at the front if you had one of them leading, then it is not working. You should not, in any way, be punished for that. DOS 1 rearranged the formations properly based on the chain order, so DOS 2 can do it as well. It should NOT be an "explorer mode only" thing.