To make sense of the notion of integer points, your scheme should be defined over $\mathbb{Z}$. What do we mean by that? Of course we should not ask for a structure map tp $Spec(\mathbb{Z})$, since every scheme has one such map. The right notion is the following.

Let $X$ be a scheme over $\mathbb{C}$; so by definition we have a structure map $X \to \mathop{Spec} \mathbb{C}$. Then we say that $X$ is defined over $\mathbb{Z}$ is there exists a scheme $X_{\mathbb{Z}}$ over $\mathbb{Z}$ such that $X$ is the base change of $X_{\mathbb{Z}}$ to $\mathbb{C}$, i. e. $X \cong X_{\mathbb{Z}} \times_{\mathbb{Z}} \mathop{Spec} \mathbb{C}$.

Now for such a scheme an integral point is a map $\mathop{Spec}\mathbb{Z} \to X_{\mathbb{Z}}$ such that the composition with the structure map is the identity. Note that the same can be done for every ring $A$ in place of $\mathbb{Z}$.

With this definition, the line $\{ x = 0 \}$ is defined over $\mathbb{Z}$, but the line $\{ x = \pi \}$ is not, basically because there is no way to generate its ideal with equations having integer coefficients. So your problem does not arise anymore.

EDIT: Abstractly of course the two lines are isomorphic over $\mathbb{C}$, so the line $r = \{x = \pi \}$ actually has a model over $\mathbb{Z}$. The problem is that this model is not compatible with the inclusion in $\mathbb{A}^2$, that is, there will be no map $r_{\mathbb{Z}} \to \mathbb{A}^2_\mathbb{Z}$ whose base change is the inclusion of $r$ into $\mathbb{A}^2$. In order to have this, you would have to ask that the ideal of $r$ in $\mathbb{A}^2$ should be generated by polynomials with integer coefficients.

As for your second question, there can be different models, that is, nonisomorphic schemes over $\mathbb{Z}$ which become isomorphic after base change to $\mathbb{C}$. So before discussing the existence of integral points, you have to FIX a model, and the points will in general depend on the model.

For instance take the two conics $\{ x^2 + y^2 = 2 \}$ and $\{ x^2 + y^2 = 3 \}$. Both have an obvious choice of a model, given by the inclusion in $\mathbb{A}^2$; moreover they are isomorphic over $\mathbb{C}$. But the integral points on the first one are $(\pm 1, \pm 1)$, while the second has none.

Finally you consider the possibility that the structure over $\mathbb{C}$ is not relevant. This is false: the base change $X_\mathbb{Z} \times_{\mathbb{Z}} \mathop{Spec} \mathbb{C}$ is endowed with a natural map to $\mathop{Spec} \mathbb{C}$, and we ask for the isomorphism with $X$ to be over $\mathbb{C}$.