Variant chests for bamboo, ancient wood, and azalea wood are all hidden and uncraftable when Woodworks is installed. The other variant wood items, such as ladders and bookshelves, are not hidden but they are uncraftable. This is likely caused by Quark's automatic overlap disabling compat feature.

Minecraft Version: 1.19.2
Forge Version: 43.2.0
Quark Version: 3.4-389

Yes that's intented. You can turn that off with the configs

But doesn't it make sense that only the items that overlap be disabled? Woodworks doesn't have variants for Quark's woods.

At the very least, the JEI hiding behavior isn't working as intended because the chests are the only thing that get hidden when disabled.

That's true. I'll see what I can do