I don't think it would need to be that complicated. At a player level there would be an unspoken rule that to properly succeed you need to take PEDs. It's still your choice, but you know without them you're not getting to the top. At a managerial level you know all your players are probably doping, but you ask no questions and hear no lies. You'll naturally pick the best performing players which are those taking PEDs. Higher than management understand that these are the risks of competing for the league/champions league/whatever, punishment is directed at the player rather than the club, and you accept the risk of loosing that asset should they get caught out, as it likely pales in comparison to falling out of the competition.
Everyone is benefiting from this gravy train and it seems even whenever someone comes out, like the recent doctor, its swept under the rug quicker than you can say EPO. In many ways the more rife it is the easier it would be to cover up, given you'll be under pressure from everyone, your team mates, your manager, your club, to keep it going or risk chucking away your 100k+ a week career. Probably not a hard choice for most tbh.
Another thing to remember is football is largely one massive old boys club. The players then go on to become managers and directors of football. They go into powerful positions at UEFA and Fifa. They're replaced by other footballers or long time football people. They are subject to practically no (or any?) external oversight. They can do whatever the fuck they want.