I don't know what IR3 is doing to cause the end product to be engine-unit while drone engine cylinder still exists and is used in the transport drone recipe but I fixed the problem by making the drone recipe use engine-unit from the base game (which IR3 renames but is still enabled) when IR3 is enabled.
In other news you may need to enable the mod setting I just created in 0.4.1 to get the output pipe from the Transport drone fuel refinery to connect to the modified pipes from IR3