They were only called at once, so no need to seperate them.

This also removes the only dereference of the NativeVertexFormat in VideoCommon, so backends may just return nullptr.

Instead we keep the loaded vertices in CPU memory.

Also:
 * Implement support for per-vertex PosMatrixIndex
 * Only update zslope constant once when zfreeze is activated.
 * Added a bunch of comments.

This is good hygiene, and also happens to be required to build Dolphin
using Clang modules.

(Under this setup, each header file becomes a module, and each #include
is automatically translated to a module import.  Recursive includes
still leak through (by default), but modules are compiled independently,
and can't depend on defines or types having previously been set up.  The
main reason to retrofit it onto Dolphin is compilation performance - no
more textual includes whatsoever, rather than putting a few blessed
common headers into a PCH.  Unfortunately, I found multiple Clang bugs
while trying to build Dolphin this way, so it's not ready yet, but I can
start with this prerequisite.)