to manage their departments in the way that they see fit. In some cases, they are less responsible and provide no oversight of unelected people that they have chosen to run various subdivisions of the dept. In other cases, they may choose to take a direct role if they feel that it is important.

Marco Rubio is the SoS. He is the head of the dept that oversees USAID. He has chosen to take over as its' director. he has chosen to freeze all wasteful and corrupt spending not involving legitimate aid projects. He is under no obligation to carry out his job or the funds allocated to him as congress never put anything in their funding bill specifying that he should.
The money saved from wasteful causes could be chosen to be given as an aid package to tax paying citizens. It could be used to provide aid to US citizens on the southern border by funding a protective wall. If congress does not approve of this, they can cut funding or they can provide specifics (good luck with that one in any adminstration as the congressmen would have to tie their names to these loathesome wastes of tax payer money - Dems were being purposely ignorant of what they knew was going on).

No presidential powers issue here whatsoever.

Again - Boom!