What you say is true about those others occurring naturally. I do know about the science, but don't know the specifics of the nfl's testing and positive test policies. However, I imagine they build in a reasonable amount of leeway. Let's say the upper limit normal level of test in a standard test is around 1000 ng/dL. If a player has 1200 ng/dL, are they gonna suspend him? Almost certainly not. It wouldn't necessarily be surprising that an elite athlete might naturally have higher test levels. And the decision that comes with negative publicity for the player, 6 games missed wages, and untold potential damage to his career.... well, I imagine it isn't made lightly. I have to believe a suspension would only come from levels that are significantly out of normal range. As far as I'm aware, the substance of note that is flagged in a test resulting in a suspension isn't usually reported or made public, so it's hard to know in each case. Lots of anabolics that bodybuilders, for example, may take are not natural, so would be easily noticed. I don't know if NFL players mostly stick to testosterone, or they use these other anabolics. But seeing the actual substance they got flagged for would help somewhat to clarify whether we should believe the excuses given.
Anyway, I think a lot of people are a bit ignorant to the level of steroid use in professional sports. Put yourself in Mathis's shoes. You're getting into your upper 30's, losing a step here and there, and there's always a young guy who wants your job. You can either juice and accept the risk of potentially getting caught, but with the upside of making millions of dollars. Or you can not juice, age and slow down naturally, and be out of a job altogether. These guys are the elite of the elite athletes, it's not surprising they will do what they can to get an edge.