Those nodules are a pain but necessary. Each sunken area in a part is a raised area in the mould that can cause a pocket of air to remain, leading to soft detail. I.E those stone grooves are raised ribs in the mould. The nodules are from holes that help allow the vacuum to suck the soft plastic sheet down into all parts of the mould around those raised areas and provide a way for any trapped air to escape. So they’re needed to improve quality. Simples.
They are tedious because of the number of them. Some are thin so when you slice them off and sand it down (not difficult all all but boring) the result can be (in a few cases not all by any means) a tiny hole which needs filling. Those on corners are thinest I find.
I haven't tried it yet but I think the answer is fill each nodule from behind, they are noticeable from the back, let the filler harden, then slice it off. Job done...maybe a swipe from a sanding stick.