The version sold at X-Plane.com & through Steam have the same features, scenery, aircraft, etc. The only differences are in how the DRM is handled to unlock you from demo mode. Steam gets new betas a little later due to the difficulties in uploading there. Steam may have better download reliability in some parts of the world that our CDN doesn't cover as thoroughly. A larger percent of the sales goes directly to X-Plane's developers if it is purchased through X-Plane.com. So there are some factors to consider, but in general there is no difference in sim features between either version.
As far as I know, most add ons are sold separately from Steam as well, or you can put any purchases made outside of Steam into the install.