it's a limitation of the system since bond levels are meant to be separate from mission levels, but for now they're the same thing since it will be properly implemented later in development
currently mission levels are mainly just cosmetic, but there is some stuff that actually utilize it like wild lamia's might makes right skill that gives her a vatk boost against the target compared to the target's level and her own
as for whether or not you'll get any bond levels from mission levels later in development, the current plan is to not keep any of them from missions (though it could always change)