The FA doesn't necessarily means he is the strongest.
But in Akainu's case, it does because he was the only one who became FA after defeating a fellow Admiral, and that was an unprecendent event that only happened once.
Also, Akainu was the one Oda choose for his comparison with Luffy and the PK, Oda could've choose Aokiji or Kizaru.
Akainu also scarred Luffy and killed Ace.
If Akainu hadn't opposed of Aokiji being FA, Aokiji would've been the FA and weaker than Akainu. The statement that FA > Admirals here only work is because Akainu is the only one who actually became FA through strength.