First, you are assuming Clemson did not test all of the players on the roster. The university absolutely could do its own drug test of all players to find out if anyone else had the substance in their system. I have no inside information, but I am guessing this has probably already been done. The university would not be required to make the findings public so I am sure they wouldn't.
Second, we know that 15 players were tested prior to the playoff so we know it was not all players that had it in their system. How many of the remaining 70 players would have tested positive is nothing but speculation and always will be.
I understand the rivalry and I can assure you if the shoe was on the other foot Clemson fans would be running with conspiracy theories too. However, there are 2 things you have to ask yourself if you really believe Clemson is using this whole investigation as a PR machine and knowingly gave these (or all) players a banned substance.
One: Why would they keep the investigation going if they knew the 3 players were guilty from the beginning? At this point Clemson would be best served to stop all investigations, celebrate the national championship, and let the positive tests just become forgotten news. By giving updates, requesting extensions, and sampling all supplements they are only prolonging the extent to which this stays in the news. If they knew they were guilty this would be a terrible idea.
Two: Why would Zach Giella take a substance that could cost him his last year of eligibility and why would Clemson risk giving him the substance? You can argue it would benefit Dexter Lawrence so I won't bother with that one. You may even be able to stretch an argument for Braden Galloway, but I really doubt that would be a sound argument. However, Zach Giella was a rising senior back up Offensive Linemen who had played 114 snaps in 2018 (in scrub time.) He is on scholarship so his education is free and he never was or is going to play any kind of major roll on the team. He is essentially a scout team OL. He now has lost his last year of eligibility (and free education) because of the positive test. What incentive does he or Clemson have in knowingly giving this guy a banned substance?