I don't know what you mean about MUXes. It's just simple abstraction to say "yeah, take this pattern of gates and give it a symbol so we don't have to draw it over and over again in detail". You're still just wiring up combinational logic...
Flip-flops and sequential logic made my brain flip-flop itself for a while though when I first ran into it. :) That really does require a different sort of thinking, since you're introducing time as a factor.
I know a lot of people who didn't really move beyond thinking about boolean logic. It's easy to reason about the larger scale component if you're reading a diagram, but it gets harder to design with them at scale.
Flip-flops and sequential logic made my brain flip-flop itself for a while though when I first ran into it. :) That really does require a different sort of thinking, since you're introducing time as a factor.