No, Jennifer was right, this works fine if you follow what she says - Compile is designed so that you can switch between standard manuscript format and ebook formats without any problem. To me, it sounds as though you have ticked “Page break before” for everything, for epub export or whatever, which you don’t need to do. You only need to use “Page break before” for instances where you need to force a page break where it wouldn’t be covered by the “Separators” pane - a table of contents is a good example of that, and it’s something you would want “page break before” set for in both ebook and SMF formats.
There would only be 20-30 lines of empty text between the text elements if you have ticked “Page break before” for them.
So: Make sure you untick “Page break before” for most documents, except for those that will need a break between them in all formats. Then set the “Separators” up as you need them, depending on the format.
If you’re still have a problem, please post screenshots of the following three things:
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The structure of your Draft folder in the binder.
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The “Contents” pane of Compile.
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The “Separators” pane of Compile.
This will allow me to see what it is you are doing, and what you need to change to get the results you expect.
By example, here is the binder from a project created using the standard novel project template:

For printing to SMF, here’s is the “Contents” pane of Compile:

Without changing anything else other than that one tick to “Page break before” for “Front Matter”, it all compiles as I expect to SMF:

And scene breaks:

Now, to compile to epub, I don’t touch anything in the “Contents” pane at all - but I will change the “Text Separator” to “Empty line” in the “Separators” pane because for an ebook I don’t want hashes between scenes, but a blank line:

And this results in exactly what I would expect in the epub (here opened in Digital Editions):

(And once I’d set up a Compile format as I want, I would save it for future use, of course.)
So, as you can see from the above, you don’t need to use “Page break before” except for documents that need different behaviour than “Separators” can provide, and in general that should be for documents that need that setting for all formats anyway, so the setting won’t need changing when you change formats.
It would therefore help if you can describe or show your specific use case so that we can see exactly where you are having problems.
All the best,
Keith