Hi. Thanks for this feedback, and apologies for delayed reply. It's been a busy few weeks. :)
As you probably saw in your other thread, I've implemented your suggestion for a setting to not use crushed stone for bio industries, defaulting to the basic production line, specifically for the megabase case. I think this should cut the number of inserters needed for silica by a good amount when using bio industries and building a megabase. I currently don't want to make too many further changes to Bio Industries compatibility because I believe they have a big new update coming out at some point in the future.
As far as silicon wafers required first tier modules, I think you are right that it requires too much. I will rebalance these shortly.
As far as the number of raw resources required for Processing Units, and advanced circuits, after last month's rebalance, I'm currently pretty satisfied with the balance. I tried to make it comparable numbers of resources to Vanilla when no prod modules are used. So, with full prod modules, it ends up as requiring fewer raw resources than vanilla.
I'll also keep your other suggestions in mind as I rebalance or add new features.
I do have some longer term plans to add an optional alternative production chain for silica that would involve quartz/sand. When finished it would reduce demand for raw stone later in the game. However, this will likely take me some time to implement.