Hi Pi-C, this is an interesting thought - currently, the silicon processing recipe uses the "smelting" crafting category as every other smelting recipe. All furnaces support this crafting category and thus all smelting recipes. Because of this i cannot simply tell stone furnaces to ignore quartz. I think this change would only be possible by using another crafting category, e.g. something like "advanced-smelting". Then, by adding this crafting category only to adv and electric furnaces, it would be possible to restrict the smelting of silicon.
Hi! I see where that's going: You could introduce such a category quite easily for your mod, without a doubt. But doing so would also introduce another point of failure if other mods are involved, and adding compatibility for each mod that creates new furnaces would be quite some effort for you. So adding another category is something that should be handled in vanilla.
I'm unsure if this change for more "realism" is really needed. I think it's also ok to use stone furnaces if you like :)
In my opinion, it would enhance the game. There are so many things you can research, and often enough, people (myself included) run through research without really using the new stuff (just think of electric furnaces: you research them, but you hardly rebuild your old smelting areas and could even launch a rocket without using them). Same thing here: I've researched advanced material processing but continued to use stone furnaces for a very long time because I concentrated on building other stuff. I would have do that sooner if it was really needed (red circuits are required for more advanced products/science but can't be made without silicon ingots). Steel furnaces as a requirement for silicon smelting would definitely limit choice (you can't skip steel furnaces even if you wanted to), but it also would make sure that more of the available toys are being played with. :-)