In general I would say that it is better to lay the stone sooner than later. The stone is always good for additional parking or storage regardless of whether a roof or enclosed addition is added.
Depending on your site and your builder, there are a few other things you might consider.
Is your cleared pad higher than the surrounding ground, level with it or, or lower? You don't want to create a wading pool along side your barn where your future addition will be. The Amish who built my barn liked to start with a level dirt pad. They would set the posts, then attach skirt boards. Rock base was hauled in after the skirt boards were attached, and the concrete was poured over the rock base. My site was a low area, so I had rock hauled in to create a firm pad before the Amish arrived. It somewhat took them by surprise, and they insisted on adding even more stone after the skirt boards were attached.
Will the addition be an extension of the main roof, or will it be at a lower level? Are you planning on having gutters on the main building and/or addition?
Would it be more economical to have at least the roof of the future addition build at the same time as the main barn?