under this setup, your quarries can't dig some other mod's blocks and even iron/gold/obsidian etc. A way to circumvent this problem would be to allow the handing of a non-vanilla tool that CAN dig those materials, (and technically the vanilla tools shouldn't even WORK under this setup. We should be giving farmers a Mattock.

perhaps a performance buff for giving miners hammers or lumber axes instead of picks and hatchets?

just a thought, could make it a conditional dependency.

Closing, was just a question after all

Quarries have an upgrading system independent of the items held by the workers.
Using "tool upgrades" will enable harvesting higher tiers of blocks.
If some modded block require a player holding a specific tool to be broken, there is no reason for a quarry to do it.

I do believe that iguana tweaks makes the mining tiers a tad more granular, and puts some blocks into the ardite & manyllyn categories, do the tool upgrades put the quarry up that high?

ahh that would make sense, I guess I didn't understand how those improved tool upgrades were to be used

The first upgrade is equivalent to iron tool level.
The second upgrade push up to diamond tool level.
The third and final upgrade will go beyond anything.