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Filesize need not be terrible, particularly if the zipping algorithm is able to recognize the similarity between the data contained in the various versions of the PDF.
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But that would requiers some specific compressing. Thus, not readeable by someting else, and that's a bad idea. If it's normal zip, you can eventually get the one file you want, and be done. Unless you make some big changes to pdf so it deals with that all by itself. (but there, you might be bettter off getting rid of pdf and starting a new format altogether.)
It would be nice to have the reader go directly to the version we want. For ePub, it's easy, if preference say "ePub", you display ePub. If preference say pdf, 5" 12px, but the proposed versions are 11px and 13px, there you have a problem.
Then the reader should stores setting for all files. (easy, we're already storing last position and bookmark in an other file).