I got the following from Thomson’s Modern Particle Physics and some other sources.
The factor 5/18 distinguishing electron-DIS and neutrino scattering experiments is a basic proof for quarks and their charges. As I understand, you use isospin symmetry to set $u_n(x) = d_p(x)$, which should be only an approximation since their mass is not identical, and you neglect contributions from s- and sea quarks. Then you take the average of the structure function for the deuteron: $F_2^d = (F_2^p + F_2^n)/2$. The 5/18 results from (4/9 + 1/9)/2, i.e. essentially the sum of z^2, the square of the charges of u + d divided by 2.
If you’d average over all p and n quarks the sum for $z_i^2$ of p + n would be: (4/9+4/9+1/9 + 1/9+1/9+4/9) = 15/9 which in turn would give as average over 6 quarks: 15/(9*6) = 5/18, i.e. the same value. Is this coincidence? Wouldn’t that be the easier way with fewer assumptions?