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The page numbers over text are not in the ePub, they are a "feature" of Adobe Digital Editions. The next version of mobile ADE will allow them to be turned off. A larger right margin also helps by pushing the page number outside the text.
I typically download Baen's MOBI version and then use Calibre to convert it to ePub. That way I can add extra CSS, like margins, to the conversion. I start with the MOBI version because usually this has the least e-book specific CSS to start with (e.g. usually justification and the font are not set in a MOBI, so you can specify these how you want). It is certainly possible to run ePub to ePub using Calibre to add extra CSS.
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