Hello, I'm making a modpack with Abyssalcraft and other things and I want to be able to control several things from config or by any other means.

• Gold/Iron/etc crystallization and transmutation. I have the whole transmutation banned, and these recipes are showing in JEI and are just eyesore that disturbs player. According to recipes, the only actually useful purpose of these is making Omothol Gateway Key and probably Dreadium, so a config option to disable these machines would be ideal. Other problems with those is e.g. Tin duplication when Bronze is crystallized
• Config option to disable progression-based tooltips
• Tool Upgrade Kits could be controlled from config. Of course, if you don't add config option, that can be done by Crafttweaker
• As well as food items - they just don't fit this mod IMO - the same comment as above
• May be a bit offtopic, but Essence of the Gatekeeper can be only obtained once, that makes its usage quite limited as I cannot gate anything beyond Abyssalnomicon - it can be only created by 1 player. Not sure what can be done here

1. Disabling them is progression breaking, so I'd rather not have a config option for disabling them. You're gonna have to remove all of the recipes through CraftTweaker (as I have an integration for that in this mod). While you're at it, you'll probably want to remove the Materializer and all of its recipes as well, since it uses crystals for all of its things. By tin duplication I take it you mean the part where the numbers for the bronze crystallizations are inverted, which I apparently mixed up and didn't notice when I initially created the crystallizer.
2. Since that has been requested before (and a config option is more convenient than a command), that's something I can implement.
   3 and 4. These are things that are gonna be removed in the future, so you might as well go the CrT route there.
3. There's a ritual to reset the temple, created for that particular purpose (well, that and failing the boss battle).

Btw bronze not only gives more tin than copper, but it gives them as if recipe was 3Cu + 1Sn (4 ingots) = 1 bronze ingot IIRC