My wife is a Cowboys fan so I pay close attention to them. While you are correct that Dak misses Amari in this offense, I believe their issues are systemic. They are supremely talented and have effective coordinators but are generally sloppy in their execution (though they were better this year than the others in this department).
The Cowboys are similar to the Rams as they have a team loaded to beat most teams but can get handled by the type of bully ball the 9'ers bring. They weren't getting past them or Philly this year. They are too good to rebuild but I believe a new head coach should be their next move