Also, the UI layout is different. For example, The top bar layout is completely different.
Stack Overflow is the exception. Check out any of the other sites; the beta site top bar layout is identical to e.g. the one here on MSE (or, say Mechanics, which is graduated but has no theme yet, or Cooking, same functionality just fully equipped with a themed design). SO's top bar is relatively new; presumably it will be rolled out to other sites eventually, but currently it isn't. SO also has a lot of other unique features that no other sites have, especially regarding the categories and tabbing in the page header, and the complexity of the review queues (triage and such, all unique to SO).
Is the "inlining videos" capability turned off on this site?
Also not a beta site limitation. This is configurable per site. You'd have to make a good case for it and petition SE to enable it. Slightly more info here. There is a query to get some stats here.
Everything else is covered nicely in animuson's answer.