I do not know the specifics of how Amman VO and/or the visa application centres (VACs) are working in Iraq and Jordan. For the most part worldwide the passport can be submitted to any VAC (but assumption/default is usually in the country where the PA resides) and is then handled by the VAC in cooperation with the VO and returned to the applicant.
Right now due to covid in many parts of the world the VACs are NOT accepting documents in person and must be submitted by courier. Even where they are taking biometrics, they are attempting to limit physical interactions.
BUT: clearly in some places they are accepting submission of passport to VAC in person. I do not know of cases where the VO (part of the embassy/consulate) is accepting in-person submission of passports for insertion of stamp. But that doesn't mean it's impossible, they adjust how things work based on local conditions.