There are two good reasons not to leave the roof down when leaving a Miata parked somewhere. First, if it rains with the roof down, the seats soak up water, and you will have a web butt for a week every time you drive the car. Second, if the sun shines, the sun will damage some of the interior trim, leaving it a chalky white. I’ve had both happen in my Miatas and while I can live with damaged trim, a wet butt is no fun.
Miata roofs wear out. Don’t sweat it. Replacing the roof is just normal maintenance.