I've found a file on the reader called /system/lib/libreadercore.so. Inside that, there is the text res:///userStyle.css. I've tried putting a userStyle.css in / (the root directory), /data, /system and /mnt/sdcard and none of these appear to work.
I've pulled apart /system/app/EbookReader.apk and system/app/EbookReader.odex but these don't seem to reference CSS much - it looks like everything is handled in /system/lib/libreadercore.so. I'll dig around in there a bit more...