paper mortar
It looks like EMI prefers the first circuit of a tier, and the universal ones have been listed as the last. This may be fixable. Near as I can tell the only way to use them is to have nothing else in your base's inventory except the universal version of a circuit. Then EMI will prefer that.
proper geode
it doesnt prefer the first circuit, it prefers what you can craft, and then has some sort of tie break logic beyond that
if you can figure out the tie break you might be able to manipulate it
paper mortar
if you can figure out the tie break you might be able to manipulate it
yes from testing in creative the tie break seems to be the order that EMI picks up the recipes. this is probably related to the order they are registered by