New testing sesh, yield values look a lot more consistent now and mods seem to work as intended.Tool used was the steel pickaxe again, used to destroy the 500hp stone block. Yield counts stone only this time.
It was mentioned somewhere that every mod always increases damage a bit,which is why I threw in all the mods in the end to check. Mother lode perk looks like it works as intended, yield seems to only decrease with that extra damage from mods now.
Flurry of blows still does not increase hit frequency for tools and seems to only apply to melee weapons. So no way to improve speed on that end for now.
As always tests performed 100% naked!
I also spelled "Strength" wrong. The shame.