So, as far as the legality of the fee change goes, in normal times, that fee is either set by Congress in the immigration act, or, more likely, set by the administering agency, presumably USCIS, in a rulemaking setting.
In normal times, that means the agency publishes the proposed fee change with a period for public comment, like this https://www.federalregister.gov/documents/2024/11/20/2024-26821/setting-and-adjusting-patent-fees-during-fiscal-year-2025
Theoretically, the public comments are taken into account and the rule either does or does not go into effect.
So, above, in January 2024, the USPTO published proposed fee changes to be effective starting January 2025 and the rule actually became final in September 2024 after a public comment period.
So, under oldlaw, the most Trump can do by EO is strongly suggest the fee change to the responsible agency, which then has to go thru some rigmarole to implement it. It's still a fait accompli, but not in much of a hurry.