Not really too arcane my friend.
Roger, like all of our modern greats, has great lungs, conditioning, speed which he keeps up over long matches and so on. Those who go on about how he is a "natural" (which all of these top guys are really in a sense) downplay this or perhaps even miss it entirely. He is rarely out of breath, rarely sweating profusely etc.
A suspicious and conspiracy minded individual could give all that a different reading than I would.
Federer shows absolutely no typical signs of someone using Peformance Enhancing Drugs. Tennis is an interesting case to investigate because it doesn't require extreme capabilities of any of the fundamental components of physical fitness (Strength, power, balance, agility, anaerobic/aerobic endurance, flexibility and coordination) except coordination which is not treatable directly via any PED. However, a variety of the components of motor fitness are required to become a tennis player, and to a greater extent when we're talking about Roger Federer, however, there is nothing truly remarkable about any of Roger Federer's physical characteristics.
Tennis isn't a sport that requires excessive amounts of aerobic endurance and that is why you will never see a tennis player post remarkable scores on any VO2 max nor Lactate Threshold test. Tennis players are good all-round athletes, but from simple observation (especially to the trained eye), you can analyse that there is nothing truly exceptional regarding tennis players (regarding CV End), and even top tennis players. Tennis players have the luxury of unpredictable sequences of play, breaks in between points and lengthy breaks every 2 games. It doesn't even take an athlete specialising in a sport which relies the majority of its physicality on aerobic endurance to be able to endure a tennis match. Take Squash players as a prime example. I am fully confident that even possibly the fittest man in our sport, Novak Djokovic, could not endure a 60 minute squash match, if he were to possess the ability necessary. The point being and to cut a long story short that there's such a thing as unnecessarily high levels of aerobic endurance and it would only take an either very lazy or a genetically less-abled individual to even consider using something like EPO or in the extreme cases (yes) Clen. Regarding the other components necessary, the same principle stands.
Despite Djokovic possessing great all-round fitness, the only truly stand-out component is his flexibility, something I believe can be trained, but something I also believe to be genetic in the case of Djokovic. I think there's many players out there who possess great levels of cardiovascular endurance (relative to tennis), take Kevin Anderson as a perfect example, but are unable to stand out from the crowd because they don't possess the other components necessary. In his case, he isn't agile enough and ability with the ball isn't there, also due to the fact he is far from agile enough. Djokovic is the target of accusations because he possesses all the physical traits which others do not and thus can showcase 6 hour displays of excellent all-round fitness in finals that others are certainly not capable of. In other words, others may be doping and exceeding Djokovic's VO2 max for example, but fly under the radar due to lack of ability elsewhere.
You mention conditioning (and vaguely), which is normally referenced toward one's body composition and physical characteristics, do I really need to explain why Federer shows absolutely no signs of PED's from this perspective?
Federer was once an athlete who possessed ideal components not because he was the fastest runner, nor the most agile, nor the most powerful, nor the most flexible, but because he had an excellent all-round base and more essentially a reading of the sport, he enabled himself to perform with exceptional efficiency. Over the years, due to the natural decrease in both physical fitness and motor fitness components (and some very noticeably more than others), he has declined overall. For the first time in his career, he showed real signs of physical vulnerability (and thus mental, of course). This is far from the typical signs of someone using performance enhancing drugs. I can assure you that there are legitimate reasons for Federer rarely seen "out of breath". 1. Players are rarely truly "out of breath" 2. He breathes just about as hard as anyone relative to the intensity of the point played. 3. Federer has always disguised his breathing by walking slowly with his head down and small, quick breaths (as opposed to Djokovic looking at the 60th row in the crowd whilst filling his lungs with air.
Nobody has any basis whatsoever to accuse Federer of doping. It is truly preposterous.