I would say that this is another good reason to rely more heavily on career civil servants and less on subcabinet political appointees. The president could have a White House of his own choosing, not subject to confirmation. Then cabinet departments and major independent agencies could have their own appointed heads with the approval of the Senate. But for the “guts” of the work of implementing White House and/or Congressional mandates, doing analysis of what program changes would entail, etc. we would do well to expand the Senior Executive Service model and rely less on Assistant Secretaries brought in from the outside. That would make it a lot more viable to reduce the number of positions requiring Senate confirmation without freaking people out about abusive or corrupt staffing decisions.
The main flaw in his arguement is if this is in place, a Republican President can nominate someone without the normal checks and balances as easily as the Democrat. I doubt Yglesias would want that.