The fact that Charlotte is less touchy-feely with you when Winona is around makes it pretty clear (to me, at least) that she recognises herself that you two have a level of physical intimacy most girlfriends would not be comfortable with. So based on that I'd say that you two falling back on that sort of behaviour when Winona isn't around may not exactly be appropriate. It just seems a bit sneaky. Maybe that's why you're uncomfortable, in part?

Also, I understand not wanting to upset your friend, but you shouldn't have to agonise about hurt feelings when setting up physical boundaries with someone, even a very close friend. There will inevitably be a shift in things when you enter a relationship. There shouldn't have to be a damage control operation. Frankly, "asking her to dial it back is going to feel like a hard rejection to her" is the sort of dynamic and response you'd see in a romantic relationship (which I know you two don't have, I'm just pointing out the blurred lines here). And conflating her finding it hard to open up to people and your availability to her for physical affection is pretty ehhhh.

I guess what I'm trying to say is that from my uninvolved outsider's point of view it does seem a bit much. Definitely talk to Winona, but you may want to start drawing the line yourself on certain things rather than accidentally ending up in a situation where you've placed all the decisions about what's okay on her shoulders. Some women may find it off-putting that you are unable to do that alone and can't recognise what's too much intimacy with a female friend.