Well, just did a bunch of experimenting - and it may be a glitch or not - here's what I found.
Preview
After a re-boot, the first time you double click on a picture in Cover Flow - it opens in Preview in front of Finder - from then on, any picture you double click on in Cover Flow opens behind Finder - it does not matter whether you quit Preview or not. On another re-boot, the first picture you open will once again open in front of Finder. At the same time, while you are scrolling through Cover Flow, you will notice whatever is in front is also highlighted in the list below. If you double click on the picture from the list instead of from Cover Flow, it opens in front of Finder every time.
Not only that, but after you have opened a picture, and next you want to open a pdf file. The first pdf you open by double clicking in Cover Flow will also open in Preview in front of Finder. From then on, every pdf you open until a re-boot will open behind Finder. Doesn't matter whether you quit Preview or not. But once again, clicking on it from the list, will open it in front.
TextEdit & Pages
Text files - opening an rtf or other text file, the first one you open in Cover Flow will open in front of Finder. From then on they all open behind Finder. However, if you quit the app instead of just closing the window, the next file you open will once again open in front of Finder. And just as in the case with Preview, at all times you can double click on any item from the list and it will open in front.
So, bottom line for a quick solution to your issue that works at this time, is just double click from the list instead of from Cover Flow .
And of course, there is always just the space bar for a quick look.