I know this is an old thread, however it is the only that appears after a search.
The answer is yes, you can change the color.
In the Ebook viewer go to:
Preference (gears icon) -> User Stylesheet
There, enter some CSS like:
Code:
::selection {
background-color: #0099FF;
color: #ffffff;
}
Click OK
That previous example will change the yellow to light blue.