I tried this with Factorio extended and was OK with some non vanilla productions did not give scrap, but was a bit surprised when I found out that smelting iron, steel, copper and stone did not. As far as I know they use vanilla recipes but I use Electric furnace mk 3. I did see that all other machines I looked at like Assembler mk 5 and chemical plant mk 3 did make scrap for vanilla production

That is another mod that we haven't (as yet) added compatibility for. I'm not personally familiar with Factorio Extended, but if it does add new furnaces, I know that we have to account for that regarding the smelting. As far as the assemblers and chem plants, those should produce scrap like the vanilla machines, as you've said, unless the mod has changed some vanilla recipes. We will add Factorio Extended to our list of mods to add compatibility for.