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Sky seem to pointing toward the fact that he is an altitude native to explain any abnormalities
They have just jumped on one possible hypothesis, but they don't seem to have tested it. At the moment, they seem confident that his blood values are natural, but they don't have any explanation for why they are also abnormal. If they wanted to know why, they would study his local family, some other close relatives who live at low altitude, some people from other countries who are 'altitude natives' etc. Alternatively, they could put a huge randomised sample population on the ABP system and they might discover that he's not abnormal at all, he's just the first person of his type to get far enough in one of the relevant sports to be on the ABP system. If 1% of humans exhibited his haematological response to his altitude regime, it would be a pretty ordinary condition but it would also not be surprising that he is the only one in the peloton to have it.
It doesn't actually have to be about altitude natives, but just about this one particular altitude native. There are freaks all over the place. Whatever it is in his genome which causes abnormal blood values could be
If he's the first person with this condition to have joined the ABP system, he's bound to look odd, but Robert Pershing Wadlow looked odd too and nobody accused him of doping.