It'll be pretty big news if the methane they use to refuel Starship on Mars originates from a fossil source :D

Elon has discussed using the sabatier process on earth to create methane from CO2 to fuel it. Presumably the motivation would be a mix of PR and practicing for mars.

ISRU methane fuel for starship is going to be eventually done on earth (and mars) for carbon neutral starship / superheavy launches.

https://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/201200...

TL;DNR: If you take methane out of the atmosphere and you put it back in the atmosphere, the carbon footprint is neutral.