The main problem with the Steam version is that TDW's generic patcher does not work with the Steam sh5.exe. However, apparently a workaround has been found:
http://www.subsim.com/radioroom/showthread.php?t=214687
Basically, the method described replaces the Steam .exe with the .exe from the 1.2 patch.
This said, I prefer Wolves of Steel over Sober's mega mod -- it is constantly updated, very stable and extremely easy to install and configure:
http://www.subsim.com/radioroom/showthread.php?t=210703