I think they look like real, fresh flowers.
They have center molds and you could dust them up in those colors. They would be time consuming to make but not to hard.
They do look real, but I don't think they stuff real flowers on the cake and in the cupcakes. Maybe they are artificial flowers?
I think they are either fresh or silk too, anyone know of a cutter that will acheive something close to this?
If you use the small daisy cutter and roll yur gum paste (or this would be a great use for cold porcelain) with 2 layers of petals you should be able to pull it off.
Looking at one of the cupcakes from the side view, I feel they either used gumpaste or maybe a modeling paste of 50/50 gumpaste and fondant and used a daisy cutter and made 2 layers, thinning each petal and layered the second set of petals between the spaces of the lower layer and let them rest in a small half circle former or similar shape to firm up and piped the center with royal icing or buttercream.