Of course, the politicos tend to remember that they are "the President's personal rep" and do not work for DOS or the SECSTATE. True for FSOs who resign to be amabassadors and then are reinstated but your point is well taken regarding the costs of going around former and future bosses.
OTOH, I knew a politico who thoght that because he was a Republican politician and had met Pres RR, he could ingnore DOS and rid roughshod over his FSO subordinates. He had a very short tenure as ambassador.

Cheers

JohnT