(MRSA is extremely contagious and going to work with it would put everyone around him at risk of getting infected, or so the doctor said).
the other times he would just man up and go to work anyway.
and the stress this is causing him, believing he will lose his job, is causing his migraines to get even worse.
MRSA might be difficult to treat with antibiotics, but it isn't really anymore contagious than standard SA. Nor is it a threat to a healthy person who might have it all over their skin along with the other SA types without knowing it.
Migraines are classed as an incapacitating headache, one does not simply man up and walk into mordor with a migraine. He might have manned up with a bad headache, not a migraine.
Stress can make migraines worse, does he wear a biteguard at night to stop him clenching and grinding his teeth? If not get one.
Anyway as to your OP, if you miss work all the time there might be a limit on self certification, after that you will need a sick line signed by the doctor. the one he sees monthly, is he actually doing anything to treat the migraines?