Steve:
Thanks for the fun site regarding training from London to Istanbul.
However, it is mentioned in that site that it is necessary to leave the train at the border station entering Turkey, get in line for the visa stamp, and then stand in another line to show passports.
I also noticed in a 2008 Paul Theroux travelogue (Ghost Train to the Eastern Star), that everyone was herded off the train at 3:30 in the morning at this border crossing to stand in these same lines.
After seeing the site you highlighted, however, my wife may start lobbying for the sleeper vs. the couchette (which we have done before, but not the best's night's sleep I've ever had).