Marco's healing isn't passive. It depends on his flames. He has to activate his flames to heal himself.
Kizaru shot Marco in his base form
After that Marco had to activate his flames to regenerate. Kizaru points out that he caught him off guard, i.e. without any flames ready to regenerate the injuries
It's always the flames. He uses the flames to deflect Kizaru's earlier attack, and to regenerate the injuries when Kizaru perforates him
And Marco's full zoan form is covered in flames. In that instance his regeneration is basically passive, i.e. he's made up of healing flames that do the work for him so he doesn't actively have to think about regenerating as the flames do that for him. Notice how he, in that form, regenerates the holes left by Kizaru's lasers immediately
