I seem to have solved my problem by using calibre to convert books to LRF format instead of EPUB.
Then I installed PRS+ which allows you to control the sizes of the differnt LRF font size settings. It seems to apply them consistently across all books. Now, when I set a book to M font size it is the same as M size for every other book.
My assumption is that LRF is a simpler format that allows the device to impose font sizes. On the other hand EPUB seems to be controlled by internal css stylesheets which is surely more flexible in theory but in practice means that every book tends to do it's own thing.
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