Maybe you aren't familiar with Vandy but I assure you - they are a highly respected university in the US. There is zero chance - none - that Vanderbilt University is creating a shadow puppet institute.
My brother and sis, who both went there, love to point out that it is called "The Harvard of the South"
Do you have any idea--any notion at all--how respected is the football program at Penn State? Why, the mere suggestion of any impropriety is such a laughable proposition that my vest-buttons threaten violent detachment.
It is amazing that you're seemingly willing to stake your reputation that there's no possibility of a conflict of interest at an institution you're only distantly associated with. But, how serious are you? What odds will you give me that at least one conflict of interest scandal shows up at Vandy over the next, say, 30 years?
It's not a binary proposition. You can have puppet institute and you can have a completely independent one. Usually you'll get something in between. I don't think that Vanderbilt's quality has a lot to do with it.
This next bit may be a bit cynical:
Even if they weren't funded by the coffee industry, however, they would have existential issues. If their whole purpose is to study coffee then I think that there will be a tendency to either promote coffee or to try to strike a balance. The latter is almost as bad as the former.
Maybe I'm wrong. Maybe they would have no problem publishing nothing about negative results if that was what they got, but I would bet against it. If they get a string of negative results (and don't lose their funding), they are going to start looking for studies that have a more potential upside to balance things out.
My brother and sis, who both went there, love to point out that it is called "The Harvard of the South"