More specifically to the point of combining the books, I'd say that Morality works great for everyone, whether they use the Force or not. Though, I might allow non-Force-users to opt-out of Morality if it better fits your narrative. Either way, it doesn't really conflict with the other systems and can just be stacked on top of whatever your core mechanic is. Duty and Obligation are sort of weird (in my opinion) when only one or two PCs have it out of a larger group. Morality works just fine all on its own since it's an individual thing.

Other than that, the mechanics seem relatively balanced against each other. It doesn't seem like it will be problematic outside some edge cases since the F&D rules are still in beta testing.

We play with everything from EotE and AoR available to the campaign. The rules work seamlessly together and combining games gives me more material to work with as GM. Because it's a EotE style campaign we use obligation. If the next one has a Rebel them we'll use duty.

Coming over from WEG, where Dark Side Points are a big deal, our group tends to be pretty conservative with the conflict. You have to do some pretty heinous stuff to get some. Lately at the end of the game, we've just gone "So, how conflicted have you felt this game? What's a good conflict score for you?"

Someone who was feeling angry or frustrated in places (but didn't necessarily act upon said anger or frustration) might get 2 or 3. Mind you, if something sticks out as particularly conflict worthy - straight up assassinating someone, failing fear checks and so on - they'll get dinged straight away, but generally we're pretty chill about it.

(That said, I think it's a pretty weak mechanic - not nearly as interesting as the obligation mechanic, as far as providing story hooks)

I don't think the Morality mechanic is designed to provide stroy hooks as to provide character growth opportunities.

Obligation and Dury are much better for story hooks.