OK, let me lay it out step by step: Anyone who’s willingly working for Trump is going to be pretty terrible. But some folks will be even more terrible than others. If Trump needs to get the people who work for him confirmed through the Senate, there’s at least a chance that they’ll stop him from getting the absolute most terrible folks. But if he just sidesteps that through acting appointments, we don’t even have that chance.
In a normal administration, those “specific instructions” don’t exist at that level. Presidents don’t give Secretaries instructions - the Secretary knows the President’s agenda and will direct the various Deputy Secretaries who in turn will direct the Undersecretaries and Assistant Secretaries , but all of this direction is is fairly broad strokes , It’s the SES , the top managerial and policymaking positions that will actually write the detailed policies and regulations and so forth. Most of these employees are career employees.
Senate confirmation or lack of it for Secretaries, Deputy Secretaries, Under Secretaries and Assistant Secretaries depends to some extent on the particular job and who was appointed. Todd Blanche can indefinitely serve as the Acting Attorney General because he was appointed under a statute that has no time limit but only allows the Deputy Attorney General ( a position that requires Senate confirmation) to be appointed as the Acting Attorney General. Anybody else would have to be appointed under a different statute, which does have time limits. As far as what happens if someone who must be Senate confirmed before a deadline isn’t confirmed, but won’t leave, my guess is the same thing that happened when a judge determined that Lindsey Halligan’s 120 day appointment as Interim US Attorney was invalid - which resulted in indictments being dismissed because only Halligan participated in obtaining them. Essentially, because her appointment was invalid, anything she did was invalid.