With the custom entry:
{
"entries" :[
{
"key": "BLOODALTAR",
"name": "research.BLOODALTAR.title",
"icons": [ "bloodmagic:altar" ],
"category": "ALCHEMY", "location": [ -3,-2 ],
"parents": [ "HEDGEALCHEMY" ],
"stages": [
{
"text": "research.BLOODALTAR.stage.1",
"required_knowledge":["THEORY;ALCHEMY;1"],
"warp": 3,
"recipes": ["bloodmagic:altar"]
},
{
"text": "research.BLOODALTAR.stage.2",
"required_knowledge":["THEORY;ALCHEMY;1"],
"recipes": ["bloodmagic:altar"]
}
]
},
]
}

And the zs script:
mods.thaumcraft.ArcaneWorkbench.registerShapelessRecipe("tests", "BLOODALTAR", 5,
[aspect:aqua, aspect:ignis, aspect:terra], bloodmagic:altar,
[minecraft:sand, minecraft:stick, minecraft:grass]);

The recipe is available before the custom research is finished. This is a major issue, since it makes it impossible to implement custom recipes tied to unique research.

Mod list:
[✔️] AutoRegLib-1.3-32
[✔️] Baubles-1.12-1.5.2
[✔️] BloodMagic-1.12.2-2.4.3-105
[✔️] Controlling-3.0.10
[✔️] CraftTweaker2-1.12-4.1.20.646
[✔️] CTM-MC1.12.2-1.0.2.31
[✔️] Guide-API-1.12-2.1.8-63
[✔️] jei_1.12.2-4.16.1.302
[✔️] modtweaker-4.0.18
[✔️] MouseTweaks-2.10-mc1.12.2
[✔️] MTLib-3.0.6
[✔️] Patchouli-1.0-23.6
[✔️] Quark-r1.6-179
[✔️] ResourceLoader-MC1.12.1-1.5.3
[✔️] tc6aspects4jei-0.0.2a
[✔️] Thaumcraft-1.12.2-6.1.BETA26
[✔️] ThaumcraftResearchPatcher-1.12.2-1.0.0
[✔️] ThaumicJEI-1.12.2-1.6.0-27
[✔️] theoneprobe-1.12-1.4.28

If you can provide a reproducing test script that doesn't require any extra mods I'll investigate this

While looking into this again I just noticed: in your research json you are using "bloodmagic:altar" as your recipe, but your crafttweaker script is adding a recipe named "thaumcraft:tests" (it appends thaumcraft: before the recipe name). The recipe name needs to be the exact name of the recipe, not the item.

Thanks!