Suggestion to add this at the end of modules.lua:

bobmods.lib.recipe.replace_ingredient("speed-module-3", "processing-unit", "advanced-circuit")
bobmods.lib.recipe.replace_ingredient("productivity-module-3", "processing-unit", "advanced-circuit")
bobmods.lib.recipe.replace_ingredient("effectivity-module-3", "processing-unit", "advanced-circuit")

, because modules tier2 are without circuits and tier3 and higher are already with green "processing-unit" circuit, so there is very high jump of technologies from modules-tier2 to -tier3 and place for white "advanced-circuit" is mising. So I think that place for white "advanced-circuit" is exactly tier 3 (or maybe tier2 and tier3, but not tier3 and tier4).
Thank you for great mod! Playing with it now all time!

"X" Circuit Boards are basically the same recipe as the advanced circuit right? The only reason that tier 3 modules take processing units normally is because the vanilla bobs modules tier 3 take the second tier of module circuit component. I personally think that the way it is currently is fine and is actually pretty good for making geometric builds. It's honestly just a matter of preference