The president can give the Presidential Medal of Freedom to anybody at any time. The choice is entirely at his/her discretion.
Medal of Freedom – Truman
The link in your question leads to a description of the "Medal of Freedom", an award created by President Harry Truman in 1945, under Executive Order 9586.
This is NOT the medal that we know today, or that President Trump conferred upon Rush Limbaugh at the State of the Union address on February 4, 2020.
A clear hint of this can be seen on your linked page in section 3, which states: "The Medal of Freedom shall not be awarded to a citizen of the United States for any act or service performed within the continental limits of the United States..."
In fact, the work that earned Mr. Limbaugh the award was done exclusively in the United States. (The Medal of Freedom was intended to honor people who served or aided the U.S. in WW2.)
Presidential Medal of Freedom – Kennedy
The award we know today is actually the "Presidential Medal of Freedom", which was established by President Kennedy in 1963, under Executive Order 11085. It replaced Truman's "Medal of Freedom".
There are various provisions in the EO describing who can receive the award but, in reality, the President can give the medal to anybody he/she chooses, whenever he/she chooses.
Sec. 2. Award of the Medal.
(a) The Medal may be awarded by the President as provided in this
order to any person who has made an especially meritorious
contribution to (1), the security or national interests of the United
States, or (2) world peace, or (3) cultural or other significant
public or private endeavors.
(b) The President may select for award of the Medal any person
nominated by the Board referred to in Section 3(a) of this Order, any
person otherwise recommended to the President for award of the Medal,
or any person selected by the President upon his own initiative.
(c) The principal announcement of awards of the Medal shall normally
be made annually, on or about July 4 of each year; but such awards may
be made at other times, as the President may deem appropriate.
(d) Subject to the provisions of this Order, the Medal may be awarded