Currently whenever you set the Config option to add an Ingot or Nugget to false, it only removes it from the creative tab and doesn't disable recipes involving the creation of that item. This is a hiccup brought on by JSON recipes as they require a condition to control whether they function.

Normally you'd just add a Condition Factory, adjust _factories, and the condition recipe file and call it a day., however since Techguns generates the recipes from code it, the conditions also have to be added and generated in a similar way.

Not worth to fix anymore before 1.13

If you do a final version for 1.12.2, I'd just ensure that the nuggets and ingots retain their ore dictionary tags so they can be used with other mods.

I'm talking from one and a half years in the future, 1.12.2 is still a relevant version, 1.13 actually didn't became a thing and was skipped, and 1.14 and 1.15, while getting more and more mods are still missing a lot of crucial mods, so while 1.12.2 is probably closer to its death than its creation it will still be a major modding version for at least a year, if not more, so it's very worth it to fix and continue developing this mod.