Two wrongs don't make a right! Bounty was far smaller and lighter than Enterprise of course, and used hydrogen thrusters to take off and land from what I recall.
Care to share where it's actually stated that the Bounty used hydrogen thrusters?
Would it really ultimately matter the size of a starship relatively to using impulse or thrusters within the atmosphere?
Would it make a difference to warp drive?
Probably not.
I come from a background of role-playing games where you have actual magic but you play within a defined set of rules. I suppose writers forgetting, reinventing, and expanding the rules beyond my expectations grates against that background.
Do you understand the idea of being indistinguishable from magic? If I took my iPad back, hell, even 100 years, and I showed them video on this small device, they would be wowed. If I took it back 500 years, they might think it was magic. The point being that we don't know how impulse or warp drive really work and if there are safeties in place to avoid damage to a planet's atmosphere.
Or as Chemahkuu states, it's simply for the sake of the plot. Yes, there is onscreen evidence to support the idea of warp drive not being used in the solar system, or in the atmosphere of a planet. Impulse too. But there is onscreen evidence support both of those being done even before Into Darkness. Maybe the warp drive in the solar system was just because of the Enterprise in TMP having brand new, untested engines? Maybe the discussion about impulse engines not being used in "The Circle" are only for Bajoran engines? And yeah, on the same argument, maybe Klingon warp engines have something that Federation warp engines don't that makes it safe to be used in atmosphere? BUT that's the only reference to that happening. Impulse in an atmosphere seems to happen a lot.
Again, all because tech of the 23rd and 24th centuries could be ultimately considered indistinguishable from magic from the eyes of a 21st century person.