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.
No, you just have to ask it in an appropriate way. There are professional survey writers who will take the questions you want to ask and then write them in a way that is very hard to misinterpret, not qualified to absurdity and not suggestive of an approved response.
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
Ok, lets try doing the calculation. The de Broglie wavelength is lambda=h/p where lambda is the wavelength and p is the momentum which is 'mv' for non-relativistc quantum. So for an atom with the same velocity as the electron the atom's momentum will be larger which means the wavelength of the atom will be SMALLER than the electron i.e. the free electron is bigger than the atom it would form.
However your argument is actually flawed because in the same environment thermodynamics requires the free electron to have the same kinetic energy as the atom. If you are capable of doing the calculation you'll find this means that the wavelength goes as 1/sqrt(mass) so even then the electron wavelength is larger than that of the atom.
So the correct, scientific conclusion is that a free electron is bigger than an atom if both are in thermodynamic equilibrium. Thinking of the electron as smaller than an atom means that you do not understand the implications of quantum mechanics or are letting your gut instincts override your rational reasoning. Quantum mechanics is often counter-intuitive and your instincts will often be wrong.
Or simply, since an electron is a component of an atom, any constituent electron will be smaller than the atom it inhabits.
You are thinking of Newtonian physics. What you say is just not true for quantum mechanics. The electrostatic potential well of the nucleus traps the electron wave and effectively compresses it over what a free electron would have in the same environment. To be more technical the addition of a potential term in the Schrodinger equation means that you end up with 3D spherical harmonic standing waves (at least for hydrogen) which have a shorter wavelength in the ground state than the free electron wave under the same thermal conditions. Still not convinced? The go read "Introduction to Quantum Mechanics" by David Griffiths which will go through the details provided you have enough maths to be able to cope with simple partial differential equations (since you have to solve the Schrodinger equation in spherical polar coordinates).