I think that the OP is worried that by folding his mat, rather than storing it the way it came from the factory/shop, would in some way damage it over the long term. I would argue that so long as you don't over stress joints and welds in the plastic it does not really matter how it is stored. If you are concerned just fold it in as many different ways as possible, and have a small repair kit handy.
I have a Thermarest that is kept rolled in my pack, but it very often got folded, stuffed, scrunched, and generally mistreated and it's still going strong.