A load is a certain amount of impedance, whether isolated or not. If the second converter is not drawing a stable load, then your MPPT will have trouble operating at a stable level.
You'll have to do some custom designing, naturally.
Isolation can mean galvanic isolation, as when a transformer intervenes. Is one in your second DC-DC converter? As a general principle, MPPT adjusts things so that maximum current is flowing through it. It doesn't care whether or not you have isolation.