Wada is concerned with any person within a registered testing pool, is taking prohibited substances at any time, in completion or out of competition.
From what it sounds like, the AFL and AFLPA have some from of policy that "random" testing only occurs after matches or within a certain time frame on match day (hence the teams can pull a player out before the test). From what I can gather the AFL testing is not random (other than maybe not all players are tested) and is not at any random time in or out of competition (which is that the WADA policy wants). This is similar to the NFL drug testing policy not fully complying to the WADA policy because the players don't want that.
The AFL is acting as cover for the players between them and the testing authority. This is the crux of the matter. They are not being subjected to the same scrutiny as other athletes who don't have a professional organisation providing that coverage (e.g. track and field athletes) and this has allowed a drug culture to continue in the competition. It's been going on for years, and I can name at least four players in the 00's (back when I was going out) I have seen doing drugs first hand.
So even though the club doctor has pulled the player from competition, WADA will still test if that player's number comes up? So what's being circumvented? You also know it's not the AFL doing the testing, it's the club doctors at a club level. This is not an AFL conspiracy.