If you change the defaults on com.apple.Safari in English.lproj, the settings will be migrated into new user accounts. At least it worked for me.
sudo defaults write /System/Library/User\ Template/English.lproj/Library/Preferences/com.apple.Safari AlwaysRestoreSessionAtLaunch -bool false
sudo defaults write /System/Library/User\ Template/English.lproj/Library/Preferences/com.apple.Safari NewWindowBehavior -integer 0
sudo defaults write /System/Library/User\ Template/English.lproj/Library/Preferences/com.apple.Safari HomePage -string “http://www.yoursite.com/”
I was copying the com.apple.Safari.plist from my admin account to the “/System/Library/User Template/English.lproj/Library/Preferences”, and that didn’t work because the keys above were gone… already migrated to whatever secret location Apple has moved them to. Adding them manually into the plist appears to work.
Original content/thread – https://www.jamf.com/jamf-nation/discussions/19668/homepage-in-safari-9-on-el-capitan
saihaynes 