org-export-before-{processing,parsing} hooks are only useful when I have
existing source files and I want to modify them in some way before I
{process,parse} them. In my case, the source files don't exist at all,
before my preparation-function is run.

Regarding the preparation-function, the use case described in the manual
is for running make to update files before publishing.

http://orgmode.org/manual/Sources-and-destinations.html

Therefore, I think it makes sense only if the source filenames are collected
using org-publish-get-base-files after the preparation-function is run.

With the above logic, maybe the order of execution can actually be
considered a bug?