Prep time does not include marinating.
Check the ingredients on your English muffins - lots of popular brands aren't vegan. For vegan muffins, try Trader Joe's.
Obviously, as portobello caps are pretty big, you're not going to be able to submerge them in the marinade. Don't worry about that. If you have a chance, spoon a bit of the liquid over top of them from time to time, or marinade in a sealed container and give a gentle shake.