What you're describing here are pedantic objections, though, of which there will always be some to any question that isn't qualified to absurdity.
For your example, the rest mass of an electron is smaller than the mass of any atom, so the wavefunction of any electron will be smaller than that of any atom at the same velocity (de Broglie wavelength) and in the same environment (the "state" you describe is a function of being part of an atom, it doesn't apply to free electrons). Or simply, since an electron is a component of an atom, any constituent electron will be smaller than the atom it inhabits.
If you contrive a complex and unreasonable enough scenario, you can change the answer to most any question (e.g., is an electron smaller than the Earth). For most exams, reasonable assumptions are expected unless otherwise stated: at standard temperature and pressure, in the ground state, etc.
The correct answer to the question is that, yes, an electron is smaller than an atom.