If we attempt to define $M_I(X)(S)$ as the set of $S$-flat ideals $I_Z$ in $\mathcal{O}_{S\times X}$, then that would not be functorial in $S$, as the inclusion $I_Z \subset \mathcal{O}_{S\times X}$ may not continue to be injective after base change (in the counter example in the other answer, restriction to the problematic fibre gives the zero map). We could impose "universal injectivity", but that is just another way of requiring the quotient $\mathcal{O}_Z$ to be $S$-flat, so then we have (re)defined the Hilbert scheme.
Another common way of defining moduli of ideals is as the moduli space for rank one stable sheaves (i.e. torsion free) with trivial determinant line bundle. The resulting moduli space is isomorphic to the Hilbert scheme of subschemes of codimension at least 2.
(I have not studied Bridgeland's paper, so I do not know the intended meaning there.)