You are maybe confusing a couple of things here.
For a FAA ATP you need to meet the hour requirements (1500 hrs) and hold in CPL in the category and class that you want for the ATP.
So you need a SE CPL IR if you want a ATP SE (pilatus PC 12, Cessna Caravan and such)
You need a ME CPL if you want a ATP ME.
You can also hold an ICAO ATP or an ICAO CPL and use it to apply for a US ATP. So no need to get a US Commercial first.
Now to the instrumnet rating:
Under FAA the Instrument rating
(not a license or certificate) is not limited to category and class.
So if you hold a PPL SE and ME VFR and you do a Instrument flight test in a ME you get both SE and ME IR priviliges.
If you hold a PPL SE and ME VFR and you do an Instrument flight test in a SE you get only SE IR priviliges.
If you want ME IR you need to then do a partial IR flight test in teh Multi where you are tested on ME specific IR tasks such as approaches with a simulated engine failure.
In the US people generally do their training in a different order then in Europe:
USA : PPL -IR CPL SE- CPL ME add on
EU : PPL - CPL VFR only - IR ME
Ask away if you have more questions.