As of version 1.1.19 (tested in 1.20.1 and 1.21.1), EMI does not draw slot backgrounds assigned to slots by JEI plugins.

Example (JEI):

Example (EMI):

In these examples, each slot was defined in the JEI plugin like this:

IRecipeSlotBuilder input_slot = builder.addSlot(RecipeIngredientRole.INPUT, 1, 1);
input_slot.setSlotName("reactant");
input_slot.addItemStacks(List.of(recipe.getReactant().getItems()));
input_slot.setStandardSlotBackground();

The call to setStandardSlotBackground() is what I was expecting to add the slots behind the ingredients.