I see there is a variable to set the roof_type for buildings. Is it possible to set building that are two stories or larger to have a peaked roof? (Like a building has when set to "height=2".)

Or is "roof_type=flat" the only option right now?

It's possible, at least the factory area in map3 has such. If my memory serves me correctly, you can use "roof_type=elevated" for that. And, all buildings with height 2 have elevated roofs by default, unless it's specifically set to flat.