Actually, they already do, and sometimes very strongly, depending on ship geometry:
So... Flight model in ED can be more "fun" and gameplay-wise consistent. But it's definitely already far behind SC's one in terms of realism and simulation detail.
Even before these atmospheric-related extensions, in SC you already could disable for example maneuvering thrusters one-by-one, and absence of each of them provided exactly expected lack of impulse in certain direction. For example after disabling all top-left thrusters, you could still normally accelerate ship "UP", but if you tried accelerate ship "DOWN", or stop it when it was moving "UP" - when top thrusters had to fire - ship started rotating clockwise, because disabled top-left thrusters didn't provide their input.
Or you could decrease thrusters (again, on a per-thruster basis) max thrust, and feel that in ship handling. For example, many say that ships in SC feel like "made of paper". Well, that's just because of insane thrusters power, temporarily set for all ships.
But you can decrease their max output to, like, 20% - and suddenly all ships in SC will handle very similarly to ED, feeling huge, heavy, with a lot of inertia, etc.
Players just don't care about it, keeping thrusters at default max output, and devs don't care about balancing thrusters while game is in development yet.
But still - SC flight model is more comprehensive, just because it "includes" ED flight model as its part, if you decrease thrusters output. But also suggests much more.
Especially now, with these improvements to atmospheric flight.