Suppose I have a proton and a neutron in an external harmonic oscillator potential well. Let us first neglect all interactions between the two: since they are distinguishable particles I conclude their Hamiltonian eigenfunctions to be:
$$ \Psi(r_1, r_2) = \phi_p (r_1) \phi_n (r_2),\tag{1}$$
where the $\phi_i$s are any HO Hamiltonian eigenfunction. Now if I do the same but thinking in terms of isospin I conclude that the eigenfunction should instead be
$$ \Psi(r_1, r_2) = \phi_{\tau = \frac{1}{2} } (r_1) \phi_{\tau = - \frac{1}{2} } (r_2) - \phi_{\tau = - \frac{1}{2} }(r_1) \phi_{\tau = \frac{1}{2}} (r_2)$$
because of antisymmetry. These two expressions are clearly different. Are these two formalisms equivalent when dealing with problems involving the strong interaction? If I introduce an electromagnetic interaction does the antisymmetry requirement decay, making $(1)$ best suited for the new problem at hand?