i don't see how that has anything to do with this mod?
in these cases (upgrading a t1 machine with one module to a t2 with two using new upgrade planner) this mod's "waiting for modules" state stops machines from working only half the time (so only while a t2 building gets delivered and placed and not when a second module is delivered and placed).
since the mod is named "Newly constructed machines wait for their modules", when upgrading a t1 machine with one module to a t2 with two machines shouldn't be stopped from working at all or they should be stopped until the second module gets delivered.