Any recipe changes made through Minetweaker are not respected by the Cook Books and the Cooking Table. The Cooking Table will even allow you to make items even if you disabled their recipe in Minetweaker.

Example: I disabled Abyssalcraft's "Chicken on a Plate" recipe because I think it's a bit boring.

However, it still shows up in the Cooking Table and remains craftable there.

Mods used:
Minecraft Forge 13.20.1.2368 (Also tested with 2454, but this changes nothing)
CookingForBlockheads_1.11.2-5.3.24
CraftTweaker-1.11.2-3.0.26
MTLib-2.0.3
AbyssalCraft-1.11.2-1.9.4-pre-4 was used in the sample above, but the issue still occurs if it is not installed.

That was fast.