What it says is

No Person except a natural born Citizen, or a Citizen of the United States, at the time of the Adoption of this Constitution, shall be eligible to the Office of President; neither shall any person be eligible to that Office who shall not have attained to the Age of thirty five Years, and been fourteen Years a Resident within the United States.

Reductio ad absurdum. Suppose you hold the premise that the US did not exist until the independent nation started. To be as generous as possible to that notion, find the earliest things that could even be considered independent actions: they started in June 1775 at the earliest (creating the Continental Army, Declaration of Causes, sending an ambassador to France a few months later). The Constitution came into force in 1789, and the first Electoral College votes were counted in April 1789. So, under the most generous interpretation of that premise, the US would have been younger than 14 years, so nobody would have been resident in the US for 14 years, so nobody would have been eligible to be President. So that premise could not have held.

I think they must have been thinking like the citizenship clause above: residence for 14 years within some state of the United States when it adopted the Constitution. Adams was born in Massachusetts; unless he left the proleptic US before he turned 14 in October 1749, he qualified. (Notice that it doesn't say they had to be resident for 14 years consecutively before election.)

(You might look in the Federalist Papers to see whether they address it, but I didn't see anything there.)

The "acting as an agent of the US" is the key part of your post. Accepting a post on behalf of the USA abroad doesn't break the residency requirement, just as it wouldn't in the case of a soldier doing a tour in Afghanistan. They aren't moving there, just there to do a job. Another example would be Dwight Eisenhower.