So you are actually correct in your math, just not in the interpretation of Gauss's law. I will first write out the math you have explained to make sure we are all on the same page.
Let's call the field from the positive plate $\mathbf {E}_1$, and the field from the negative plate $\mathbf {E}_2$. Let's put our Gaussian surface on the plate with a charge density $\rho$. Then on the surface between the plates the total field is $E_1\hat x + E_2\hat x$, and on the surface outside of the plates (closer to plate 1) the total field is $-E_1\hat x + E_2\hat x$
Now let's use Gauss's law, where we only need to worry about the surfaces mentioned above due to symmetry.
$$\frac {Q_{enc}}{\epsilon_0}=\int (E_1\hat x + E_2\hat x)\cdot(dA\hat x)+\int(-E_1\hat x + E_2\hat x)\cdot(-dA\hat x)$$
The integrals are very easy to evaluate.$^*$ If we do this and divide by the area of the plate enclosed by our surface we get.
$$\frac{\rho}{\epsilon_0}=E_1+E_2+E_1-E_2=2E_1$$
which is what you discuss in your answer. We end up with a true expression, but not the expression we wanted. Why is, this?
Notice what happens here: the $E_2$ terms cancel. This is because the field due to any charges outside our Gaussian surface does not contribute any net flux. It does not mean that the field between the plates itself is not influenced by the second plate, which can be seen by the fact that $E_2$ stuck around until it cancelled after calculating the total flux.
What you would really want is a Gaussian surface that contains "an equal amount" of both plates , but also has a surface between the plates that the total field flows through. I can't think of a surface with this property. So the easier way to go is treat each plate separately and then add the fields to get the total field.
$^*$ This is where my answer differs from the one by @enumaris. You actually can factor the fields out of each integral, since they are still uniform over the surfaces in question.