I don't believe it gives little girls that impression at all. If any of us thinks back to when we were little and tried on some lipstick, for example, I think we realize that we weren't even thinking in terms of "beauty with or without make-up" (the way adults concerned about this issue do). We were just happy to feel more grown-up but also happy to have noticed the look that adding color gave us.
I really think little girls see something like make-up the same way we might see an evening dress: It's something we see as making us look special on some occasions. It doesn't occur to us that we "must be unattractive" the rest of the time. Most of us remember having, maybe, a special sundress and sandals that made us feel far more special than we felt when we wore a shorts-and-top set. I think little girls like to feel special and pretty, and I think it helps the self-esteem of anyone who knows what it's like to feel special and attractive. I think it helps kids learn that when it comes to people who feel special and good about themselves, they are among them; rather than being among the people who have never experienced that positive feeling.
When she tries on the make-up she's most likely aiming to see how pretty she'll look when she adds the color. Telling her she looks pretty tells her she's accomplished what make-up is supposed to accomplish. Imagine how she'd feel if people said, "Oh, that (that you're so happy with) looks awful."
To be candid, I think little girls' self-esteem is more likely to be hurt when they find their smart, capable, sensible, little selves being treated as if they're fragile flowers to be protected from the world, or else as if they're too dumb to know the difference between being told they're beautiful when they're dabbling with make-up and still being comfortable with who/what they are without it. :)