Obviously these are relevant things to consider in analyzing the integrity of the situation. If one happens to believe that an organization like Simmaron wouldn't receive extensive HHS funding without serving as a CAA-like toady to the predominate CDC/NIH viewpoint (even if only indirectly through having only their viewpoint-aligned studies funded), then naturally these associations are incredibly pertinent to the independence and integrity of advocates.
Now, the concern over the financial ties implied now amounts to saying that there's an added incentive, perhaps, to retain those common views, and to perhaps move closer together with that alliance of viewpoints. BUT...
It doesn't imply that their advocacy is necessarily compromised, but such conflicts of interest must be considered.
It's also important to always keep in mind that advocacy really doesn't have to be compromised by this. OK, so the emphasis of writing may be affected (though it doesn't have to be), but also, just as the parties move closer to each other in views, and influence each other, so the advocate (Cort) moves closer to having access to the ear of Simarron and the HHS. What he says will very likely have influence on them, just as what they say has influence on him, as they work together as a team and learn from each other.
In any potential conflict of interest like this, there are potential threats, and potential opportunities too. So long as the potential conflicts of interest are declared, this is simply the way the world works and it is present in every situation where an individual is employed or paid, in the same way. So IMO there's not much to make a fuss about here, really, just something to bear in mind when assessing what people say.