First of all, thanks for making this mod because it contains exactly what I wanted to change about AngelBobs, and you really nailed it with both your mods.
Because you remove the beacons in the modules.lua file and remove the electronics assembling machines in the assembly.lua file and don't load either when Circuit Processing is present, the result is that MK2/MK3 beacons and electronics assembling machines are enabled when playing with Circuit Processing. I'm not really sure if this is intended, but I don't believe so.