No, there isnít any doc about it. The Proofread Page doc is very messy and work on documentation is something really needed (itís something that any advanced editor of Wikisource can do).
# yes the bottom of nsPage body is trimmed (itís normal normalisation of wikitext content). If it breaks pages we can disable this normalisation.
# you can add a default footer content in Mediawiki:proofread page_default_footer (it doesnít works currently because of a bug but it should be fixed soon (in the worst case at next Tuesday deployment)). †If you want to customize this value for a specific index, just add a new field called 'Footerí (the ID is important) in†MediaWiki:Proofreadpage_index_data_config with header:true. en.wikisource use this feature.
# basically yes
# yes you have to if you use the action=edit API. Iím working on an other API action that will allow to edit only the body and/or the proofreading level (and that will be used also by the VisualEditor when itíll be integrated)
† † †† by Thomas

Thanks for details; usually we are learning by "try and learn" and explicit details like those you give save hours of tries!

# trimming bottom of the page: IMHO it's an excellent idea. The simple trick to add (manually or by a script launched at onSubmit event) a tl|nop at the bottom of the page when needed to force the closure of a paragraph at the bottom of the page and saves many transclusion issues.
# in the meantime, since we have to activate such a "final cleanup routine", it would be easy to "take a look" to body text and to add a references tag (after a new line) into the footer only when needed (t.i. when text contains a ref tag or a template building a ref tag - an infrequent case.
# I only use wikipedia.Page .put() method to edit pages by bot, I don't know if it uses API action=edit, but anyone writing by itself scripts to edit nsPage is used to test carefully the header-body-footer stuff so that here some try-and-learn will clarify the matter.

I'm going to copy-and-paste your† message.... as soon as this unavoidable "bug explosion" will rest, I've many other questions for you.... but not now. :-)

Thanks again.