No, there is no violation of "intensivity". The reason is that $K_{eq}$ depends on $n$, and changes in one cancel the other out.
For example, consider the electrolysis of water:
- $$\ce{2H2O_{(l)} -> 2H2_{(g)} + O2_{(g)}}$$
The equilibrium constant for this reaction is $K_{1}=\frac{[\ce{H2}]^2 [\ce{O2}]}{1}$ and if you wrote out each electrochemical half reaction separately, $n$ would be 4.
Now consider this reaction:
- $$\ce{4H2O_{(l)} -> 4H2_{(g)} + 2O2_{(g)}}$$
The equilibrium constant is now $K_{2}=\frac{[\ce{H2}]^4 [\ce{O2}]^2}{1}=(K_1)^2$. If you wrote out the half-reactions for this reaction, $n$ would be 8, twice as big. But the $\ln K_{eq}$ term would also be twice as big, since $\ln K_2 = \ln{(K_1)^2} = 2 \ln K_1$.