I'm doing something like this with mcxToProfile (https://github.com/timsutton/mcxToProfile). I use it a lot to create custom configuration profiles to replace older MCX settings in my JSS. Just run mcxToProfile.py against ~/Library/Preferences/com.apple.Safari.plist (after you setup Safari to your liking) and you will get a mobileconfig file that you can edit and upload to your JSS.
You will want to edit it so it only contains the ManagedPlugInPolicies setting, this is an example (not full output) for com.oracle.java.JavaAppletPlugin. This will set the configured site to run the java applet in unsafe mode with no user prompt.
<key>mcx_preference_settings</key>
<dict>
<key>ManagedPlugInPolicies</key>
<dict>
<key>com.oracle.java.JavaAppletPlugin</key>
<dict>
<key>PlugInDisallowPromptBeforeUseDialog</key>
<true/>
<key>PlugInFirstVisitPolicy</key>
<string>PlugInPolicyAsk</string>
<key>PlugInHostnamePolicies</key>
<array>
<dict>
<key>PlugInHostname</key>
<string>Your_HostName</string>
<key>PlugInPageURL</key>
<string>https://Your_URL</string>
<key>PlugInPolicy</key>
<string>PlugInPolicyAllowWithSecurityRestrictions</string>
<key>PlugInRunUnsandboxed</key>
<true/>
Once you have the profile to your liking, just upload it to your JSS and scope it out to your clients.
Allen
That seems like a handy work-around; I'd much rather my JSS had the functionality that is present in Profile Manager, and not have to re-upload an entire config profile for every modification, though.
I'm using 9.3.1 does anyone know if there is a fix for this. I am doing the same, using mcxtoprofile, uploading, then editing. Not ideal.