Create a VPrj file with Comskip

That’s correct, it only copies the EDL files to the output folder since most programs only use EDL files.
Having said that, since the VPRJ file is created by your custom comskip.ini when MCEBuddy runs it, have you tried adding a simple CustomCommand to copy the VPRJ file from the working folder to your destination folder?

Something like this:

CustomCommandPath="c:\windows\system32\cmd.exe"
CustomCommandParameters="/c copy /y "%workingpath%\%originalfilename%.vprj" "%destinationpath%\%convertedfilename%.vprj""
CustomCommandHangPeriod=30
CustomCommandCritical=true
CustomCommandUISession=false
CustomCommandShowWindow=false