Sorry, Melissa, but let me say what I MEANT to say ...
The flange is at the toilet's drain. The base of the toilet, well, it's the base of the toilet.
As for the gap at the flange, you could caulk it. Just clean it as best you can. When you set the toilet back on the flange (with the wax ring too), I say caulk that too. Why, you ask??! Well, if you grouted the toilet base, then if the toilet ended up rocking a little, then over time, the grout will crack and you'll have a rocker instead of a toilet! If you caulk the base, the caulk will 'give' just enough, and pretty-much flex back into place. I've shimmed the base of toilets before, then cauled around it, even if they rock BEFORE I bead the caulk.
Be sure to seal the grout under the toilet before you finish installing it. You know what will happen if you don't.