Making Pier configurable is something I spent a bit of time on.
Pier-Jetsam-Environment package (in pieraddons) moves everything that
configures Pier into the PRFrame class heirarchy. You choose your chosen
PRFrame class in the seaside/config app.
The Frame class can be coded to provide default environments (which do
not appear in the tree to users), template environments (when the user
adds an environment it is initialised automatically), stylesheets, and
loading of js libraries.
The package comes with an Admin Frame which presents the same as the old
pier admin.
It has frames which can be subclassed to use blueprint css.
It also has a frame which implements 7 common layout options that you
can style and switch between.
There is even a top level frame which allows subsections of the site to
switch to use different frames.
Keith