These are the new prototype adjustment points being added in the recent patches. I will attempt to include every one into the settings menu, which is a good time to standardize the options into groups to help organize them.

Version 2.0.56
QualityPrototype::
default_multiplier
inserter_speed_multiplier
fluid_wagon_capacity_multiplier
inventory_size_multiplier
lab_research_speed_multiplier
crafting_machine_speed_multiplier
crafting_machine_energy_usage_multiplier
logistic_cell_charging_energy_multiplier
tool_durability_multiplier
accumulator_capacity_multiplier
flying_robot_max_energy_multiplier
range_multiplier
asteroid_collector_collection_radius_bonus
equipment_grid_width_bonus
equipment_grid_height_bonus
electric_pole_wire_reach_bonus
electric_pole_supply_area_distance_bonus
beacon_supply_area_distance_bonus
logistic_cell_charging_station_count_bonus
beacon_module_slots_bonus
crafting_machine_module_slots_bonus
mining_drill_module_slots_bonus
mining_drill_mining_radius_bonus
lab_module_slots_bonus

CraftingMachinePrototype::
quality_affects_energy_usage

MiningDrillPrototype::
quality_affects_mining_radius

BeaconPrototype::
quality_affects_supply_area_distance

CraftingMachinePrototype::
LabPrototype::
MiningDrillPrototype::
BeaconPrototype::
quality_affects_module_slots

Version 2.0.58
CraftingMachinePrototype::
crafting_speed_quality_multiplier
module_slots_quality_bonus
energy_usage_quality_multiplier

So far I have the major adjustment points finished, I will keep working on this tomorrow and hopefully wrap up the rest of them!
So far I have finished and tested these:
QualityPrototype::
default_multiplier
lab_module_slots_bonus
tool_durability_multiplier
beacon_supply_area_distance_bonus
beacon_module_slots_bonus
mining_drill_module_slots_bonus
mining_drill_mining_radius_bonus
crafting_machine_module_slots_bonus

CraftingMachinePrototype::
quality_affects_energy_usage

MiningDrillPrototype::
quality_affects_mining_radius
quality_affects_module_slots

BeaconPrototype::
quality_affects_supply_area_distance

CraftingMachinePrototype::
LabPrototype::
BeaconPrototype::
quality_affects_module_slots

I dont think I will be setting the 2.0.58 options for crafting machine prototype itself, because they overwrite the others.
The remaining options are looking fairly simple so I hope to have that done soon.

Big updates to the overall look of the settings menu! It looks way more readable, and has the item icons in the setting strings so its a lot easier to see where each section begins. I hope the new style of setting menu will be a lot easier to use. I am excited to release the new version when I am done!

Everything is now live! I hope everyone enjoys the newly expanded customization!