From Inventor 2010, it is possible to start Inventor with set of application options settings you want just like the /p option we have in AutoCAD.
Use the below switch in the target path of Inventor shortcut
/IMPORTOPTIONS="path where the Application Options XML file is stored"
for example if you have exported your application options to C:\compatible.xml
"C:\Program Files\Autodesk\Inventor 2011\Bin\Inventor.exe" /IMPORTOPTIONS="C:\compatible.xml"
Double click on the shortcut will open up Inventor with the application options set in compatible.xml file.
Note - This currently works only on 32 bit operating systems not on 64 bit.