The University has requested that I make some skin / dialog changes to
core SharePoint pages including CreatePage.aspx.

What is the best practice for modifying the application.master from
which these pages inherit?

Would it be better to implement my own applications that inherit from
our custom master page? Is there a way to globally override page
references that would normally go to CreatePage.aspx to instead be
redirected to CustomCreatePage.aspx?

Perhaps I could install the publishing feature, and create a feature of
my own that requires the Publishing feature but overrides some of its
functionality?