[Fredej]

My understanding is that the "encourages" part relates to agencies that are independent and are therefore not directly under the control of the president. He therefore cannot directly order them to do anything.

However, from what I could gather from news interviews, this has not been published without the collaboration from those agencies, who in general are on board with the changes.

[ascagnel_]

Correct, the President is actually fairly limited in how much control they exert over regulatory agencies -- such agencies are created by Congress, commissioners are nominated by the President and confirmed by Congress, and commissioners report back to Congress.