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Minecraft version: 1.12.2
Wizardry version: 4.2.11
Environment: Single & Sponge server

Issue details:
CraftTweaker/CraftTweaker#1077
mezz/JustEnoughItems#2098

CraftTweaker

val runeStone = <ebwizardry:runestone:*>;
val runeStonePedestal = <ebwizardry:runestone_pedestal:*>;

recipes.addShaped("Waystone", <waystones:waystone>, 
[
    [null,              runeStone,              null],
    [runeStone,         <waystones:warp_stone>, runeStone],
    [runeStonePedestal, runeStonePedestal,      runeStonePedestal],
]);

JEI

Minecraft

Other mods involved:
Crafttweaker: 1.12-4.1.20.589
JEI: 1.12.2-4.16.1.302

Hmmm okay... there's nothing special about runestone metadata compared to any other metadata blocks apart from 0 not being a valid value. Does crafttweaker have a way to specify a range of metadata values?

That is done by :* which they are doing already, it is the vanilla wildcard metadata, and works fine on things like wool and planks (and I would assume more, I had the user test wool specifically and it worked).

No way apart from for 1 to X. And it's what I'm using

val runeStone = <ebwizardry:runestone>.definition;

for meta in 1 to 8 {
    <ore:blockRuneStone>.add(runeStone.makeStack(meta));
}

val runeStonePedestal = <ebwizardry:runestone_pedestal>.definition;

for meta in 1 to 8 {
    <ore:blockRuneStonePedestal>.add(runeStonePedestal.makeStack(meta));
}

And that works? If so, then it must be because of meta 0 being missing.

Yes. It's ok.

And that works? If so, then it must be because of meta 0 being missing.

Great, in that case I assume allowing meta 0 as a variant (even if it's unobtainable) will fix this.

It's generally safest to assume that players will find a way to get invalid items, particularly when other mods are involved.