I was playing a campaign with Angel's and Bob's mods and found a problem with Copper Ore. Even without Productivity Modules, if you just build Angel's highest tier Copper Ore processing you end up with
12 Copper Ore
=> 6 Processed Copper
=> 8 Copper Pellets
=> 24 Copper Anodes
=> 24 Copper Ingots
=> 240 Molten Copper
=> 6 Copper Sheet Coil
=> 24 Copper Plate

So you have a 2:1 ratio of Copper Ore to Copper Plate, even without any productivity mods. (With Bob's productivity mods, you can easily get >2x copper plate to copper-wire coil).

The problem is in the Coppery waste byproduct and the Waste Byproduct.
Coppery Waste becomes 1:1 Copper Ore, and Waste Byproduct splits into 50% Iron ore and 50% Copper ore.

Each Blue Science (Spectrum Analysis) needs 1 Femto Laser Array and 1 Atomic Sensors Array.
Femto Laser requires Femto Laser Foci which takes 5 Copper Plate, producing 1 Coppery Waste product, and one Femto Laser taking 8 plate, and producing 3 Coppery Waste Product.
It also takes Basic Electronic Board which requires some copper. Factorio says that each Laser Array consumes 22 Copper Plate (and should produce 4 coppery waste).
Atomic Sensors Array consumes 12 Copper plate and produces 5 waste.
So that should be a total of 34 plates consumed, and 9 ore produced. With just Angel's, that becomes 18 copper plates, with 100% productivity (5 tier 4 in an Assembly Machine 5), it becomes 36 total plates produced, and for 34 consumed.

Military Science similarly uses 6 copper plate in the Weapons Testing Module, but produces 2 coppery waste, and 7 mixed waste (3.5 copper ore). That's consuming 6 plates to produce 5.5 copper ore. So even without productivity modules, just the 2:1 with Angel's refining creates more copper than it consumes. The brass in the sub-plate also consumes half an ingot to create a plate (without productivity) but produces 1/2 an ore in waste.

I do understand the idea of adding complexity to make science interesting, but producing the item that you are consuming is always going to cause problems once Productivity Modules come into play. I've been taking them out of everywhere I could find, but the fact that Military over-produces copper when you use the 'efficient' production chain is a problem.

seems might be good idea to remove waste from some products, when using bobs angels, since in vanilla you don't have any other ore except iron, copper, but yeah, replacing stuff with other materials, when playing with bobs and angels indeed should lead to lower or zero production of byproducts.

i did reduce waste byproduct to max 3 pcs (usualy it's 1 or 2), even for vanilla. while waste byproduct idea is neat, it needs to be modified to match actual process. i have some ideas, but it will take some time to balance it. still i did not want to complete remove this, hence the reduction.

as for eff/production, those will create crap results with everything, due they nature, creating something from nothing ... i would rather see such thing as improvement in technology/recipe, rather than just put some gizmo into your factory and you get magical 200% more stuff.

we can discuss balancing ideas on forum, locking this for now.