Mod Suggestion

[JasonMcRay]

Some form of one item storage might be nice to have. Like Storage Drawers (https://minecraft.curseforge.com/projects/storage-drawers)

mods.storagedrawers.OreDictionaryBlacklist.add("craftingQuartz");
mods.storagedrawers.OreDictionaryBlacklist.add("itemNetherQuartz");
mods.storagedrawers.OreDictionaryBlacklist.add("itemCertusQuartz");

You might want to use this for minetweaker integration to prevent Nether quartz to Certus Quartz

Feel free to check IT2 script for drawer controller and compacter recipes if you will deem it necessary.

As for the config. I recommend changing B:invertShift=false to B:invertShift=true because a lot of ppl are used to this behaviour from Jabba (this changes if by holding shift when taking items out it should take whole stack out or only item)

[RedNicStone]

I thought GT had his own type of storage drawer....
The storage drawer mod is a bit OP in my view, but ok.

You might make a pull request on your change to certus/nether Quarz...