Measuring body size in flies/insects
I think you are correct, but I'm not an expert in Diptera/Drosophila morphology. Since the prothorax (pronotum) and metathorax are greatly reduced in flies, you mostly see the mesonotum in dorsal view, and this includes the scutellum. Personally, I think it would have been more accurate of them to label this structure mesonotum, or at least dorsal mesothorax length, since mesothorax could just as well imply a ventral view (mesosternum).

More information can be found at this webpage: Flies - Morphology and anatomy: Thorax, which state that:


  The mesonotum occupies most of dorsal view of the thorax. In order anteroposterior we can identify four parts, called as follow (McAlpine, 1981): prescutum, scutum, scutellum, and postnotum. The scutum is the most large, condition considered apomorphic for the entire order of Diptera.


Also see this picture of the mesonotum from diptera.net