I think, instead of just saying "make yourself at home" and leaving it at that, it might be wise to be a bit more specific, since people have so many interpretations of the phrase. For example, I might say, "If you want to grab a soda or something from the fridge, feel free. Here's the powder room if you need it, and if you want to watch TV while petting the cat, you can use the one in the study, we keep the remote here." (I'm imagining someone who stops by every day for an hour or so.)
In my mind, this would set some reasonable parameters that they could extrapolate from, which would help both of us. With these instructions, there should be no reason for them to go upstairs and use the master bathroom, for example, or use any other TV in the house, or the computer. They can eat what's in the fridge, but shouldn't defrost and cook a chicken, or open the liquor cabinet. Some things might still be a little vague to them--can they use my plates and glasses? Could they read one of my books instead of watching TV?
I would rather someone erred on the side of caution, or at least gave it some thought first, and then asked me about it/mentioned it to me later--"FYI, I brought my fast food dinner in and used one of your plates so I wouldn't get crumbs everywhere. I rinsed the plate and put it in the sink afterwards. I hope that's okay." Or, "Just to let you know, Fluffy was in a weird mood today and I had to dig through the master bedroom closet to look for him. I shut the master bedroom door when I left so the cats couldn't get in there again."
I wouldn't be very comfortable with someone who used things without thought or who made assumptions about what I meant that were more on the "liberal" side. When you're at someone else's house (unless you've been there many times and are very close to them) I think you should just be more cautious and careful by default, and ease into being more relaxed with the owners' encouragement. When the owners aren't there, and you are, I think it's especially important to think about "appearing responsible," beyond actually being responsible, and to communicate clearly with the owners about what you do there.
In this case, the cat-checkers might have made a reasonable assumption about having permission to drink the OP's wine, but they weren't responsible about looking up the brand first and they didn't leave a note explaining their plan--really, how long would either thing have taken? So my thought would be, "What are they going to make an assumption about next, and leave me in the dark about?" On the other hand, the incident might indeed make the OP feel like they can now communicate more clearly about limits and feel assured that the cat-checkers had good intentions, so she might see it as a positive outcome. I think either response is reasonable.
It's kind of interesting to think about, really.