Whle I can work around this with crafting table recipes, it seems my approach is ineffective with AW2's "research recipes".

closing, released several releases back

I have this fixed in dev, actually using "chest" ore dict as well as I have fixed all the other stuff that could be ore dicted.
the research recipes are here btw https://github.com/P3pp3rF1y/AncientWarfare2/tree/1.12.x/src/main/resources/assets/ancientwarfare/research_recipes
They use similar support to vanilla recipe ingredients, but are enhanced with the understanding of what research they are dependent on and can support ingredients with stack sizes greater than 1.