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It is simply that epubs and printed documents have little in common execpt the content. A printed page has each word, paragraph, heading in a specific location on a specific page.
A epub reflows, as you change the size of the text, so text that would be on page 5 in the original could be on page 9 in an epub.
You might consider using Merger, a program which merges html pages, mostly used to turn a website into a book. But you could unzip your epub (an epub is only a specialized zip file) and then use Merger to merge everything together. It is a bit cranky, but probably easier than using cut and paste which might introduce extra line spacing, paragraph markers or breaks when you paste it back.
Some of the shortcomings of epubs can be addressed by agressive indexing (for books that require indexing) and Sigil has a special function for it.
There is no print book however, where you have a large print versions and a normal print version at the same time. With epubs you can have often 3 or more text sizes to suit the reader.
This make it hard to make a set of assumptions of what you should do with the text for printing.
A pdf, however unglamorous, solves this problem by being printable and to some extent reflowable. If it is for personal or small organization use, it is a good solution, as most ereaders and tablets can display pdfs.
For your purposes as I understand them, I think I would finish laying out the printed book as you want it and use it as your standard to work the epub around to capture all the important elements of layout in the printed version. But some things like tables display poorly as they do very badly when increased in size.
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