Then I ran over beyond compare and found out that it supports a "rule based" comparison that ignores byte differences but checks if the content is the same. In the gui, I could successfully compare my pdfs as "rule based equal".
So, now my question for TestComplete:
I created a script function that uses Win32API.WinExec( "[... whole command line]") and it seems to be doing something, but WinExec does not return the result from beyond compare (I expect "3"), but something bigger than 32.
So, how can I call an external process from script and do something with the exist code the process returns?