Administrative agencies administer the laws enacted by Congress after the fact at the direction of the POTUS. Federal admin. agencies can't really bypass another branch. The chief administrator (POTUS) can by executive order only, and Congress can challenge it immediately, taking it to Justice, or dealing with it internally.
Most of these agencies were created by past POTUS's through Congress (or by Congress) in such a way that a chain of command and proceedures must be followed (
https://www.scribd.com/document/264...e-Process-in-Federal-Civil-Service-Employment) in order to fire anyone not directly appointed by the POTUS himself. A Director of an agency can refuse to fire someone under his/her command and the Pres has little recourse beyond firing that director and getting someone else in there to do it.
As for the Pres getting into just any ol' files, no, he can't. As Hunterpoet stated, there is 'need to know' as well as classification. Presidents do not have blanket 'need to know'. Anyone with military insight knows this and the reasons for it.
Anyway, I may agree with you that some agencies were designed to give the POTUS undue and unconstitutional power, if you were to give back some real evidence of this.