Are you saying that they are hired as political appointees but somehow switch to civil service without having gone through the civil service qualification and hiring process? How is that done?
Yes. The head of a particular agency, with permission from OPM (who must approve the hiring of any person that served as a political appointee in the last 5 years), can hire a political appointee directly into a civil service position. Since OPM is currently controlled by Trump, it stands to reason that permission is already rubber stamped for any such moves.
It is the same method used by Michael Ellis (who was unqualified for his appointment in the first place) to move from an appointed position on the National Security Council in the White House over to be hired as a legal counsel with the NSA. He is the guy that tried to classify John Bolton's book, and was one of the guys that was feeding intelligence over to Devin Nunes on alleged Trump election survellience. Kash Patel (who started in an appointed position as one of Devin Nunes' own appointed stooges) was just hired by DOD to become Chief of Staff for Trump's new Acting Defense Secretary Chris Miller. When Biden replaces Miller, he'll be shuffled off to some other DOD job. And, Trent Benishek was hired from an appointed position in the White House over to serve as the general counsel at GSA (who is still holding up the presidential transition process by refusing to announce Biden is President-elect).
All three started out as political appointees and are now working directly for Uncle Sam in $100,000+ per year positions. It will be very difficult for Biden to get rid of any of them as long as they keep their noses clean and stay away from any overt political actions.