Disabling fast boot (system settings) programmatically
Here's a batch file registry hack that should do what you want. 0=disables and 1=enables fast startup. This leaves regular hibernate alone. I use this as part of my prep script for new machines that have SSDs and thus already boot-up super fast.
reg add "HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Power" /v HiberbootEnabled /t reg_dword /d 0 /f