Quark will remove the recipes for all variants of its woods (Ashen, Azalea, and Trumpet) and non-wood items (Nether Brick, Purpur, and Prismarine Chests).

It also removes the recipes for Vertical Planks even though Woodworks doesn't add any.

I also noticed that it doesn't auto-disable plant crates and the Gunpowder Sack if Thermal Expansion/Cultivation are installed.

Log:
latest.log

Oh, and the REI info for the Sturdy Stone has a typo. Should be cannot.

Would also be nice if all the filled Seed Pouches were hidden from REI's item panel by default.

(and the Stick Stack should have a burn time of 1,000 to match other storage blocks' formula of 10x the material's burn time - but at minimum, it should respect the setting you can change in the mod config. I've set it to 1,000 and it won't change).

So anty overlap works on a per module basis. Its not a silver bullet, its meant to be as a nice automatic feature for those that dont care to configure their mods. If you want to configure stuff you should do it properly with the mod configs.
For vertical planks i can remove it since thats its own module.
For the crates i could add anti overlap there but will also disable all other stuff form compressed blocks module.
REI shows all stuff that is in Creative inventory, thats how it works i believe.

Not sure about that last issue

Yeah, i don't know why stick stacks don't have the correct burn times either - but it's been an issue ever since they were added, as far as i can tell.

I did manually re-add the recipes, but i figured i'd report it since it felt like a bug to me.

Vertical planks change would be nice, and don't use the other 2 so i got nothing to say there.

Perhaps the variant blocks setting could have 2 sub-sections? (one for wooden chests and one for non-wood chests) - but like i said, i did fix it myself so it's not that big of a deal.

Whoops. Sorry for missing this. I did not mean to open a duplicate. I understand why this behavior happens. But it would still be nice. I suppose this is more of a feature request than a bug report then?

Still, I should probably open up another bug report about how the ladders and bookshelves still appear in creative when they probably shouldn't.

If this does get addressed, I think it would be also nice to have an option to use the variants from quark instead of woodworks. I actually like quark's designs a bit better and would prefer to use them since they also have the chaining ladders compatibility and all while woodworks does not.

Lol I saw that