According to the Bus4You-homepage extra luggage can be prebooked. An extra piece of luggage (max 25 kg) on top of the one piece plus hand luggage included ARN-Karlstad costs SEK49, so I'd probably go for the bus.
It's probably what I'll plan to do. Even if I miss the 9:15am bus, there is another one two hours later. As much as I like walking around Gamla Stan during my layover, being able to relax and avoid Centralen is worth the extra kronor.