Yes, Matt Smith is the 11th Doctor. Yes, he's also on his 13th and final life. It is not complicated

and if Steven Moffat is making it complicated then that's sad.

Look. A Time Lord can regenerate 12 times for a total of 13 lives. The first time the Doctor regenerated was when he changed from the First Doctor to the Second...

Regeneration - Actor - Doctor - Life

     0.  William Hartnell - 1st Doctor - 1st life

1. Patrick Troughton - 2nd Doctor - 2nd life
2. Jon Pertwee - 3rd Doctor - 3rd life
3. Tom Baker - 4th Doctor - 4th life
4. Peter Davison - 5th Doctor - 5th life
5. Colin Baker - 6th Doctor - 6th life
6. Sylvester McCoy - 7th Doctor - 7th life
7. Paul McGann - 8th Doctor - 8th life
8. John Hurt - War Doctor - 9th life
9. Christopher Eccleston - 9th Doctor - 10th life
10. David Tennant - 10th Doctor - 11th life
11. Meta-crisis ("Journey's End")/David Tennant - 12th life
12. Matt Smith - 11th Doctor - 13th life

No, the events of "The Impossible Astronaut" aren't a problem because it was a shapeshifting robot duplicate. And the Doctor using regeneration energy to heal River's wrist in "The Angels Take Manhattan" just has to be residual energy from the time she burned up all her regenerations saving his life in "Let's Kill Hitler." (Because the alternative is that Moffat invented the War Doctor after Season 7a.)