Simplest answer: physics.
As someone who's owned both soundbars (JBL Bar 5.1, Polk Magnifi, Vizio) and full Atmos/stereo setups in the past three years, I have some experience.
Physics because:
1. Driver size. Conventional surround systems have much much larger drivers (at least 4", mostly 5.25-6") than soundbars (1-2" typically). This reflects in poor dynamics, clarity and obviously inferior "feel" of sound.
2. Soundstage. Cramming all your speakers into a 3-4ft space means that a soundbar can't come close to the separation and sound stage of a conventional stereo setup, forget a surround one.
3. The center channel. Most soundbars (especially budget ones) are 2.1 configurations, not 3.1 as they ought to be. A dedicated center makes a world of difference in vocal clarity.
Those are the most significant differences, IMO.