As the title says, even when "Output byproducts" (bzlead-byproduct) is disabled, the mod will still modify all furnaces to have at least 2 output slots.
Specifically, on line 10 of data-final-fixes.lua, the mod only checks for the presence of other mods, and not for Lead's own setting (unlike line 37 of lead-recipe.lua where it correctly checks util.me.byproduct() to choose which results list to use).

Thanks. This was intended just to manage complexity a bit, but given the suggestion, that will be a nice change for player clarity. It will be in an upcoming update.