The actual file is /System/Library/StagedFrameworks/Safari/Safari.framework/Versions/A/Resources/R eader.html
I am not an expert of CSS, but I modified it without any apparent consequences. Here is the process (do so at your risk):
0. Close Safari
1. Locate the file in the afore-mentioned folder
2. Drag it on your desktop (this will create a copy)
3. IMPORTANT: Rename the file in the original folder to Reader.html.backup or similar (this will keep the original file, should anything go wrong) - you'll have to type your admin password
4. Open the Reader.html on your desktop with TextEdit
5. Find the following section (about midway through)
body {
margin: 0;
padding: 0;
background-color: transparent;
-webkit-user-select: none;
overflow-x: hidden;
6. Replace the third line with
background-color: rgb(40, 40, 40);
This is dark grey, but you can obviously use any other rgb combination. Black is 0, 0, 0.
(Unfortunately I haven't found a way to restore the transparency—it looked way better)
7. Save the file, and copy it back in the original folder (you will have to type in your password again.)
8. Open Safari and off you go!