Yeah, they are separate systems. But last time I was there when the FP system was down, they told us we had to show proof (
MDE screen) of our FPs to use the FP queue. And with MDE down... ugh, that sucks. I needed to book some FPs today, but at least I'm not in the park without FP/MDE, that would be much worse.
Given how integral WDW has made MDE/FP into the Disney experience and with the budget (and profits) that WDW has, you would think that they could (would) make a stable system. If only they didn't lay off their IT team and replace with outsourced employees.