The issue of spurious CT states in TD-DFT is substantially ameliorated using range-separated and long-range corrected density functionals, yet measures of electron-hole separation and exciton size remain important tools for analysis of excited-state calculations. In the present work, we demonstrate that some widely used charge-separation metrics are not invariant under unitary transformations of the occupied or virtual molecular orbitals (MOs). This implies that their numerical values depend on the choice of representation. This has been pointed out before, but the present work explores the numerical and conceptual implications of this result for the first time. Dependence on the choice of orbitals is not an esoteric point, as we will demonstrate substantial numerical differences (including nonsensical results) using several common MO representations.