In the implementation, mapshot render uses the list of mods from the current Factorio install. It means that the render can include or exclude some mods compared to what the save was using in reality. Ideally, mapshot render should get the list of mods used by the save and only activate those.

A save file does contain the list of mods which were in use at the moment the save was created - this is displayed in the UI. Unfortunately, this information is only contained in script.dat, which format is largely an implementation detail of Factorio. That makes it hard for mapshot render to find out which mod to activate or deactivate at the moment.