I can’t seem to find a lot of standard team stats, like points allowed, rushing yards allowed, etc. Am I missing something or are they just not in the game?

A lot of team stats are under the team stats page. Other stats are in the bottom left corner for current season... and in the bottom under league leaders you can see the top 5 of some other stats. Under Season Recaps you can see past history of point, yards, etc.

And all stats are exportable via options and clicking on Export CSV/Access

You can also see a lot in the weekly under matchup on each game, and incredibly in depth on the play analysis tool.