I've had rubbers stored for 26 years in a box, curled up in a triple loop, with absolutely no harm being done. That would have been impossible with the trim left in, and I can't imagine how the trim would preserve the rubber anyway. They would have got bent, and the rubber would have been exposed to the elements too.
Plus, you can't properly clean the rubber with the trim in. Don't use a wire-brush (much too coarse). Remove any old sealing compound before going over it with fine steel wool (I use 0000). It takes about 2 hours to do one rubber properly, very hard on your fingers, but the rubber looks brand-new afterwards.
I didn't treat it with anything, and it doesn't seem to have hardened at all - just surface oxidation which the steel wool removes.
Evan - welcome to drop by and see my car sometime. You know my email.