Absolutely, and I do have the pictures to prove my point, though I, too, erred, in making my comment overly complex! (As if the rules for how the Monarch is to display her flag (-s) isn't complicated enough!)). I should've simply stated that, while the Monarch's not present onboard, the Flag Officer Commanding (usually a senior Rear-Admiral or junior Vice-Admiral) flies his pennant from the foretop. When the Monarch is onboard (or maybe I ought to say was onboard, since the yacht was decommissioned in 1997!), the Admirality Flag (Anchor Flag is always flown from the foretop. If the Duke of Edinburgh is present, the display can be either his rank flag (full Admiral's flag) or the Union Jack on the mizzen. If the Monarch's not present, then she follows the same practice as any regular RN vessel, with the difference that she's always ranked as a flagship. Notice that one of the pictures shows the flagshroud of H.R.H. the Prince of Wales too.
Anyway, here's a good selection of pictures: