I'd pick Dark mode for eye comfort, especially for users who work at night or in low-light environments.

I'm not convinced that it's a binary choice - what about an option to schedule mode changes based on time of day?

I'd choose Dark mode for eye comfort, but what about accessibility implications for users with visual impairments?

I'd pick 'System default for user preference' as it respects users' personal settings and device configurations.

I'd pick 'System default for user preference' - users should be able to choose what works best for them, and forcing one mode might alienate some users.