Does xmr-stak use Stratum? Using Wireshark to analyze packets sent by xmr-stak, I found them to be inconsistent with those of Stratum (https://en.bitcoin.it/wiki/Stratum_mining_protocol).

From Wireshark:

{
  "method": "login",
  "params": {
    "login": "33vberEwdZYECfGsbqNJQC7M1MCHYT9Mjm.alpha0",
    "pass": "x",
    "rigid": "",
    "agent": "xmr-stak/2.4.2/e10e8e6/master/lin/nvidia-cpu/aeon-cryptonight-monero/0"
  },
  "id": 1
}


According to Stratum documentation:

{
  "method": "mining.authorize",
  "params": [
    "33vberEwdZYECfGsbqNJQC7M1MCHYT9Mjm.alpha0",
    "x"
  ]
}


If not, what protocol does xmr-stak use?
Yes Monero mining pools generally use the Stratum protocol for communication between the pool and the miners. However a modified version of the Stratum protocol is used. I've yet find proper documentation like the one you've linked, so your best bet is to look through the source code for the exact definition. 

Also there is a separate Stackexchange for the Monero community, so your likely to get even better help there.