p.s I am aware you can force install chrome extensions using Google Apps Admin - Which I have tried, but A. The users need to be signed into chrome for this to work, which not all our users do. and B. I would still need to use Jamf to add the intranet address to the extension, Which I have tried to do (using composer), but have had no success.
I've had success creating a custom configuration profile that will force install a chrome extension. I have not however played with setting any settings for an installed extension. You can look at the settings you can set using a configuration profile by going to this site. There is an option on that site that says you can set the new tab behavior, but it doesn't work. That site lists a bunch of other things you can manage with a configuration profile as well.
I've included an example configuration profile that you can use as a template to get started. You would create this configuration profile and upload it to the JSS. I had a hard time figuring out how to get the force install to work because you have to get the last bit of the extension URL and the chrome extension update site.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>PayloadIdentifier</key>
<string>com.company.profile.chrome</string>
<key>PayloadRemovalDisallowed</key>
<true/>
<key>PayloadScope</key>
<string>System</string>
<key>PayloadType</key>
<string>Configuration</string>
<key>PayloadUUID</key>
<string>2016-09-12-07-13</string>
<key>PayloadOrganization</key>
<string>Your Company</string>
<key>PayloadVersion</key>
<integer>1</integer>
<key>PayloadDisplayName</key>
<string>Google Chrome Policy</string>
<key>PayloadContent</key>
<array>
<dict>
<key>PayloadType</key>
<string>com.apple.ManagedClient.preferences</string>
<key>PayloadVersion</key>
<integer>1</integer>
<key>PayloadIdentifier</key>
<string>com.normandale</string>
<key>PayloadUUID</key>
<string>121-qasd</string>
<key>PayloadEnabled</key>
<true/>
<key>PayloadDisplayName</key>
<string>Custom: (com.google.Chrome)</string>
<key>PayloadContent</key>
<dict>
<key>com.google.Chrome</key>
<dict>
<key>Forced</key>
<array>
<dict>
<key>mcx_preference_settings</key>
<dict>
<key>ExtensionInstallForcelist</key>
<array>
<string>CHROME EXTENSION;https://clients2.google.com/service/update2/crx</string>
</array>
</dict>
</dict>
</array>
</dict>
</dict>
</dict>
</array>
</dict>
</plist>
So where I have the ExtensionInstallForceList it should look like this, the example below is the Ardusat Chrome App:
<key>ExtensionInstallForcelist</key>
<array>
<string>gdclcnobolflddkbmimlehkcopmcnmfj;https://clients2.google.com/service/update2/crx</string>
</array>
From what I've read, the update site doesn't change for extensions that are downloaded from the Chrome Web Store. Again, I don't know if you can manage the actual extension from this, as I haven't tried. This would atleast get you one step closer and it doesn't require the user to be in their Google Work account. You can create this configuration profile as a computer level profile and it just get installed for everyone on that computer.