8 days ago - Shurenai - Direct link
It doesn't.

The difference is in what the perk effects.

Miner 69er affects the damage done by the tool; Not the damage the block takes from the tool. So it still works against buildings and stuff, because the buff is to the tool itself.

Motherlode affects the reward from the specified block types; So it's effect only applies to the mentioned block types (Ore, Stone, Terrain blocks, Trees) when using any specified tool (axe, pickaxe, shovel, chainsaw, auger).