The way I took it was that "break up" still meant being on "a break from the relationship." Not a full break up. Thinking about it, I can see how it can be interpreted as an actual break up and I think her saying "break up" was her just using the term to mean "on a break" or thinking about if they should fully break up or not. I feel like it all stems down to Ross not bothering to hear Rachel out. First when she said they should take a break from each other to when Mark came over, he refused to let her explain that he came over as a friend or at least that's what she thought Mark's intentions were. I can't remember if that was what Mark was intending or not. Also when she came over and asked to be his girlfriend again, that could've very well be her wanting to end the break from each other.