If there is no chance to fix the problem quickly in API, maybe a workaround in WS-Export may be introduced?

At the moment, all Wikisource-based e-books which contain references seem to be broken.

I did some tests, the problem does not occur when we transclude content using the standard way:
https://pl.wikisource.org/api/rest_v1/page/html/Rest_api_test_01 (OK)
vs
https://pl.wikisource.org/wiki/Rest_api_test_01 (see: https://pl.wikisource.org/w/index.php?title=Rest_api_test_01&action=edit)

However, transclusion using the tag (used on ws) <pages ... /> the problem occurs:
https://pl.wikisource.org/api/rest_v1/page/html/Epub_Test (NOK!)
vs
https://pl.wikisource.org/wiki/Epub_Test (see: https://pl.wikisource.org/w/index.php?title=Epub_Test&action=edit)

or

https://pl.wikisource.org/api/rest_v1/page/html/Mohikanowie%20paryscy%2Fca%C5%82o%C5%9B%C4%87 (NOK)
vs
https://pl.wikisource.org/wiki/Mohikanowie_paryscy/ca%C5%82o%C5%9B%C4%87

This indicates, in my opinion, a problem related to the handling of the Prooofread extension by rest_api or the parser - someone familiar with the Proofread extension should also look at this.

I kindly ask for any help - currently, 100% of e-books with footnotes generated by wikisources (pl, en, fr ...) are incorrect.

After some investigation, it seems this bug has been introduced by the migration to Parsoid. It's likely that Parsoid fully parses wikitext from custom MW tags like <pages>, including references, before including them in Parsoid output. Adding native support of <pages> to Parsoid might fix this problem (or not, not sure...).

Yes, any extension that deals with wikitext will need to implement functionality for Parsoid. See https://www.mediawiki.org/wiki/Parsoid/Extension_API#Parsoid_API_for_extensions ... We probably need a phab task for Pages that is a child task of T258838

In T319258#8349895, @ssastry wrote:

Yes, any extension that deals with wikitext will need to implement functionality for Parsoid. See https://www.mediawiki.org/wiki/Parsoid/Extension_API#Parsoid_API_for_extensions ... We probably need a phab task for Pages that is a child task of T258838

We definitely need such task to resolve the problem before Parsoid becomes the main content parser in Wikisources. Otherwise many pages will be silently broken like many ebooks have been broken for few months, now. Who can/should do this?