I do not know anything about skinguard, but  I am curious about your vet’s connection between ear infection treatment and runny nose/watery eyes. That sounds like treating for a URI (upper respiratory infection) would be good to explore. It’s possible your rabbit has/had both an ear infection and a URI, and/or one is related to the other.

Metacam is an anti-inflammatory, so it could be used to help reduce any swelling and congestion?

Oh yes, an ear infection can be painful. But as Wick suggested, the pain meds can also be used to reduce inflammation. The eyes, ears, and sinuses are all connected so an infection can start in one place and migrate to the others. What you are describing seems more consistent with a URI… but I assume the vet saw infection in the ear upon examination.

Ear infection due to very narrow ear openings is unfortunately a very common problem with lop rabbits, so you will need to keep an eye on this. As LBJ says, the middle ears are connected with the mouth and nose and throat via the Eustachian tube, which means that bacteria can travel from the mouth and nose to the middle ear. There is also a possibility that an outer ear infection causes wax and pus to build up outside the eardrum, putting pressure on it. The pressure can eventually cause the ear drum to break.

Ear infections can be very painful, but rabbits often hide pain well.