As for the prisoners at Mardin- If you have killed the beastlords between the prison and the exit, they survive and run away. If not they get mowed down.
There is a bonus mission, yes. It can be made avaliable with either downloading the bonus.exe file (you can find it in the download section) or by manually editing the bos.cfg file, locate the line which says something like bonus.....=false and make that =true and it should work fine...