Phil - I wasn't suggesting that you use the Ens.Deployment.Utils but rather the Studio.Project utilities.  This will allow you to put in any specific classes that you wish to include (including the Production definition which should include all the pointers to the new BOs, BPs, and BSs) so that you can cherry pick what goes into your next environment.  I am not familiar with the Ens.Deployment.Utils so I can't compare the approproaches

There are different kernels but other than that you should be able to run the same ObjectScript code on both platforms and it will behalf identically.  If you are going to be doing file interactions, then I suggest using the %File library class which will make your code portable between Windows and UNIX file systems.  Likewise if you are calling out to other executables, you will need to instrument your code to call out appropriately based on your platform.