I have encountered a bug where the crafting recipes are still available for the stone tools. No apparent errors that I can see.

Modlist:
abnormals_core-1.16.5-3.1.1.jar
AppleSkin-mc1.16.2-forge-1.0.14.jar
Aquaculture-1.16.5-2.1.18.jar
astikorcarts-1.16.5-1.1.1.jar
AutoRegLib-1.6-47.jar
BetterCaves-Forge-1.16.4-1.1.1.jar
BetterMineshafts-Forge-1.16.4-2.0.3.jar
BiomesOPlenty-1.16.5-13.1.0.465-universal.jar
Bookshelf-1.16.5-10.0.7.jar
Clumps-6.0.0.22.jar
collective-1.16.5-2.26.jar
comforts-forge-1.16.4-4.0.1.0.jar
CraftableHorseArmour-1.16.X-1.4.0.jar
create-mc1.16.5_v0.3.1c.jar
cuneiform-1.16.3-1.2.4.1.jar
DoggyTalents-1.16.5-2.0.1.4.jar
endergetic-1.16.4-3.0.0.jar
gravestone-1.16.5-1.0.4.jar
Hwyla-forge-1.10.11-B78_1.16.2.jar
infernal-expansion-forge-1.3.jar
itemzoom-1.16.4-2.3.0.jar
jei-1.16.5-7.6.4.90 12.50.04 PM.jar
jei-professions-1.0.0-1.16.4.jar
JEIEnchantmentInfo-1.16.4-1.2.1.jar
jeiintegration_1.16.5-7.0.1.15.jar
journeymap-1.16.5-5.7.1.jar
More Totem Effects 1.16.5 v1.4.jar
MouseTweaks-2.14-mc1.16.2.jar
notreepunching-forge-1.16.5-4.1.3.jar
Quark-r2.4-311.jar
QuarkOddities-1.16.3.jar
QuarkOPlenty-1.16.5-1.2.1.jar
repurposed_structures-1.16.5-2.6.6-forge.jar
SereneSeasons-1.16.5-4.0.1.91-universal.jar
spiders-2.0-1.16.4-1.0.4.jar
StorageDrawers-1.16.3-8.2.2.jar
swingthroughgrass-1.16.4-1.5.3.jar
terraincognita-1.16.3-1.6.4.2.jar
Tips-1.16.5-4.0.7.jar
travelers_index-1.16.4-1.0.2.jar
villagernames_1.16.5-2.9.jar
YungsApi-1.16.4-Forge-6.jar

Alright, so in conclusion, I am not going to specifically override Quark's recipes. Both mods make a modification to the same recipes, Quark does so in a bit of a painful way (but their options are limited by the non-existence of conditional tag entries). So you can either write the datapack to resolve conflicts, or fix as mentioned above.

Find out what mod is overriding the recipe then. As that's the exact same thing NTP does, and whichever mod loads their data last will "win".

At a hunch: try quark.

Yes, I just disabled quark (along with quarksoplenty and quarkoddities), and that fixed it.

just made the ticket

So

• The stone tools I believe are caused by quark's "better stone tools" option. This is from these recipes.
• Quark does something very odd here, in that they replace the minecraft:stone_tool_materials tag in said recipe with minecraft:cobblestone, in such a way that means the recipe gets forced on (as NTP data loads before quark by default).
• I think they should fix this and just add the cobblestone tag to the stone tool materials, then we wouldn't have this issue.
• I could also (I believe) put a dependency to load NTP's resources after quark. But this is rather awkward and I'd rather avoid this if possible (as it solves this specific issue and no others). Which is probably what I'll end up doing because I don't believe quark is going to change this (based on a prior conversation about this exact recipe I just pulled up).

In general,

• you can make a datapack (even copying how the NTP recipes work), which disable wooden and stone tools. Then load this after both mods, and choose whatever combination of NTP and quark features you would like.

Okay, I will make a ticket on quark's github and bring this up. I'll tag you in it as well so you can get notifs. I just fear that they changed that tag for a specific reason that they will not be willing to change. Perhaps a compatiblity patch would work, but I'm not a modder and I don't know the logistics of that.

Anyways, I'll make a ticket and hopefully that'll change this predicament.