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The page_template.xpgt file can (and should) simply be removed. You should also remove the links to it that will exist in all the files. You should complain to your printer about their inclusion of this file, which simply interferes with the way the book is rendered and interferes with cross-platform compatibility.
This file only affects the rendering on ADE-equipped readers and represents a very early attempt to extend the page model used for ePub beyond the very limited version offered by CSS 2. Adobe dropped all development on this many years ago, and has only maintained support for reasons of compatibility. It should not be used for new publications.
If it's used properly, it can offer some powerful features, but this only happens in conjunction with specific coding of the css. I have yet to see a single publication that actually uses it as Adobe envisaged. Instead, a default page template is inserted which serves no purpose other than to mess up the page margins that you set in your css stylesheet.
The desktop version of ADE supports multiple columns automatically, so you don't need it for that. While the page-template file offers a more sophisticated and flexible way of specifying the layout of of multiple columns, that will only happen if you edit it yourself and set the parameters appropriately. The default file that they toss in provides no advantage.
Again, my advice is that you complain about this loudly, and if they give you any stick, PM me and I'll send them a stiff email as well. There is absolutely no excuse to be integrating this into new books.
As for your cover image, Liz's advice is right. It sounds like your problem is simply that the image you've used doesn't have enough resolution. The page-template file certainly won't change anything here.
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