I think if a couple chooses to set up a honeymoon fund, or house fund or whatever, with a company, it's up to them to read the fine print about when they get the money and what happens if XYZ. Although I would expect the company hosting the website would get a cut, it's hard to imagine one would have a policy of, "If you don't reach X amount of money, we get to keep it all!" But, like I said, I think that's the couple's responsibility to figure out. If I wanted to give to a gift fund like that, I wouldn't worry about contingencies like that--I'd figure the couple must be fine with losing 5% or something being nonrefundable or whatever, because they chose to set it up. Just like if they register for a gift I think is ugly, or for something that I had and didn't like--shrug, they say they want it, I want to get them something they want, I assume they've looked into it since they actively had to click the button to put it on the registry.
Gifting brings out funny feelings in people. For me, I've started to feel like it's not X or Y that's rude (say, having a honeymoon fund) it's how the actual person behaves about it. Someone could have everything look completely correct and traditional on the surface (say, no registry of any kind, no mention of gifts on any invitation, etc.) and still be a rude gimme pig who, behind the scenes, tells everyone they better cough up the dough, cover their plates, etc., because that honeymoon or gourmet kitchen isn't going to pay for itself! Whereas I can imagine another couple has a honeymoon fund and several "thing" registries, but they're completely gracious about any and all gifts they receive (or no gifts), and the registries are more like lists of things they're happy to buy for themselves no matter what. I feel like I've seen it go both ways personally, especially the former, where everything looks right but then you hear what's below the surface, and their comments really made me feel both exploited and unappreciated.