You can’t actually customize setenv.bat (or any of the other files in the distribution) when you create a deployment, but you add a SiteDeploy.bat file to the install. setenv.bat is set up to call SiteDeploy.bat:

rem Verify the existence of the SiteDeploy.bat file
if exist "%XSI_BINDIR%\SiteDeploy.bat" call "%XSI_BINDIR%\SiteDeploy.bat"

To add a SiteDeploy.bat file to a deployment, you need to configure the Softimage deployment:

In the Additional Files section, expand Application\bin, and then click Browse to locate the SiteDeploy.bat file (which must exist somewhere already):