In complicated systems this just leads to literally everyone being unhappy: You get vocal users who's weird combination of settings lead to edge case bugs, leading to devs getting stretched thin playing whack-a-mole and neglecting the needs of base case users.

Yes, but this is a practical rather than an inherent issue. You’ll see these crop up anytime you have a lot of people using something.

Honestly not really. Complexity breeds bugs simply due to surface area, and complexity grows exponentially with features (as in, each boolean option you add doubles the number of states your system can be in).