Theoretically, the President can. The President is the custodian of the security clearance since clearance itself is really derived from Executive Order 12968. So, the President can simply simply grant clearance eligibility to literally anyone. The only limitation I see will be Dept of Energy clearance, since it is derived from an Act in 50’s (I will need to double check on that or anyone can freely comment on that).
Senate confirmation does not negating the need for clearance only with exception to Supreme Court Justices. Members of Congress, President and Supreme Court Justices are constitutional officers; thus, they don’t go through the process. All others will need to, including political appointees.