There's a difference between "knowing better" than to dope, and "knowing better" than to be transparently obvious about it, which may be the kicker. Vaughters has had a knack of getting good late blooming performances out of people you mightn't expect it from - Hesjedal, Vande Velde, Wiggins, and so on. But although he's inadvertently outed his own riders before, and he's had riders test positive while riding for him including those who were supposedly committed to his clean riding team vision (the whole thing being about redemption for all of those ex-USPS guys and so on, which was the narrative the team built themselves around), Jonathan Vaughters does know better. There is no real obvious evidence out there that Michael Woods is any more or less suspicious than anybody else around there; quite often late bloomers at a variety of success levels come from other sporting endeavours - Richie Porte from triathlon, Primož Roglič from ski jumping, Maria Canins and Tara Whitten from cross country skiing, Benjamí Prades from biathlon - so his emergence at a comparatively late age isn't so much of a red flag since he has moved across from another endurance-based discipline (unlike Rogla, who comes from a discipline more about explosiveness), although as noted athletics is one of the sports with a reputation as negative as that of cycling. Vaughters has had those things happen that suggest all may not always be sanguine at Slipstream Sports (insert name of whichever team he's managed to successfully cannibalize to keep the team going here - how he manages to be the man in charge of a team that needs to seek out a merger so often and successfully manages to convince another team to merge with him AND let him keep the reins is testament to his negotiation skills), but because he knows better, he doesn't have seven guys all going on absurd mountain breakaways like CSF-Navigare (remember the Fedaia stage with 3 CSF guys in the group of 5?). Because he knows better, he doesn't have Mustafa Sayar forgetting to hide the needle marks. Because he knows better, he doesn't have Ricardo Riccò passing out after trying to self-transfuse at home.
The thing is, nothing Michael Woods does is implausible; he has shown himself to be a quick learner in road cycling and very good in short-to-mid-length steep ascents, of precisely the kind that the Ardennes and the Vuelta specialise in. He was good from the get-go at the WT level in that kind of race and as he's got smarter he's improved his results in the type of races that he is good at. There aren't any real red flags that would suggest he's a doper, but he's competitive enough in an era where trust in the sport is massively eroded that he's sticking his head above the parapet.