In exercise 16.4.B of Vakil's notes, he establishes that the group of automorphisms of $\mathbb{P}_k^n$ is $PGL_{n+1}(k)$. This I can manage to show, but in the remarks following the exercise he asks why this does not work over an arbitrary base ring $A$, and I have a hard time to see why. I have three questions and would be grateful if someone can comment on them:
1) First, is it true that $\pi^*O_{\mathbb{P}_A}(1)\simeq O_{\mathbb{P}_A}(1)$ if $\pi:\mathbb{P}_A^{n}\to\mathbb{P}_A^{n}$ is an automorphism? Over a field $k$, this holds because an automorphism induces an isomorphism on Picard groups. So a generator must be sent to a generator, but I do not understand the Picard group of $\mathbb{P}_A^{n+1}$, so I can't see if this generalizes. In any case, if it is true, please give an argument. If it's not, please give a counter-example.
2) Does it make sense to define $PGL_{n+1}(-)$ as the functor that sends $A$ to the set of $(n+1)\times (n+1)$ invertible matrices over $A$ modulo multiples of identity? If so, is it representable (possibly in some sub-category of schemes over $A$)?
3) If $PGL_{n+1}(A)$ does not parametrize automorphisms of $\mathbb{P}_A^{n+1}$, what does it parametrize?
4) Is there a good description of automorphisms of $\mathbb{P}_A^n$?
2) No. Here is a topological analogy, which I learned from MO: instead of commutative rings, let's think about C*-algebras of continuous functions on compact Hausdorff spaces $X$. Then $\text{GL}_n(C(X))$ is equivalently the space of continuous functions $X \to \text{GL}_n(\mathbb{C})$, for example. The "correct" definition of $\text{PGL}_n(C(X))$, e.g. the one that makes it representable by a space, is therefore the space of continuous functions $X \to \text{PGL}_n(\mathbb{C})$.
This is not the same as $\text{GL}_n(C(X))$ mod its center; the discrepancy is described up to homotopy by an exact sequence
$$H^{0}(X, \mathbb{C}^{\times}) \to H^{0}(X, \text{GL}_n(\mathbb{C})) \to H^{0}(X, \text{PGL}_n(\mathbb{C})) \to H^{1}(X, \mathbb{C}^{\times}) \to \cdots$$
associated to the short exact sequence
$$1 \to \mathbb{C}^{\times} \to \text{GL}_n(\mathbb{C}) \to \text{PGL}_n(\mathbb{C}) \to 1$$
of topological groups, where by $H^0(X, G)$ I mean homotopy classes of continuous maps $X \to G$ and by $H^1(X, G)$ I mean homotopy classes of continuous maps $X \to BG$, where $BG$ is the delooping of $G$. Here $H^1(X, \mathbb{C}^{\times}) \cong \text{Pic}(X) \cong H^2(X, \mathbb{Z})$ is the Picard group of continuous line bundles on $X$, so the exact sequence tells us that the obstruction to lifting an element in $\text{PGL}_n(C(X))$ to an element of $\text{GL}_n(C(X))$, up to homotopy, is given by a line bundle on $X$; roughly speaking this is because there is a $\mathbb{C}^{\times}$s worth of lifts locally but no guarantee that it is possible to patch them up globally into a consistent global lift.