Add Sites to Google Chrome's Pop Up Blocker's Managed Exceptions

I have not done it myself, but I think (not sure) that the com.google.Chrome.manifest file may be able to help you do this in a managed way. But maybe others have tried to do it and it doesn't work? I'm not certain.
I just poked around in it and I see a few keys:
PopupsAllowedForUrls and PopupsBlockedForUrls. I would look there as a start

@milesleacy Configuration profile might be your best bet, i used mcxToProfile to create this:

<?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>PayloadContent</key>
    <array>
        <dict>
            <key>PayloadContent</key>
            <dict>
                <key>com.google.Chrome</key>
                <dict>
                    <key>Forced</key>
                    <array>
                        <dict>
                            <key>mcx_preference_settings</key>
                            <dict>
                                <key>DefaultPopupsSetting</key>
                                <integer>2</integer>
                                <key>PopupsAllowedForUrls</key>
                                <array>
                                    <string>http://www.tomholbrook.co.uk</string>
                                </array>
                            </dict>
                        </dict>
                    </array>
                    <key>mcx_targets</key>
                    <array>
                        <string>user-managed</string>
                    </array>
                </dict>
            </dict>
            <key>PayloadEnabled</key>
            <true/>
            <key>PayloadIdentifier</key>
            <string>MCXToProfile.bceaecbb-e125-42f0-b827-85066b2b01c3.alacarte.customsettings.d8e1254e-7c7e-4f50-955d-467f41a49f8b</string>
            <key>PayloadType</key>
            <string>com.apple.ManagedClient.preferences</string>
            <key>PayloadUUID</key>
            <string>d8e1254e-7c7e-4f50-955d-467f41a49f8b</string>
            <key>PayloadVersion</key>
            <integer>1</integer>
        </dict>
    </array>
    <key>PayloadDescription</key>
    <string>Included custom settings:
com.google.Chrome pop-up settings.
</string>
    <key>PayloadDisplayName</key>
    <string>Chrome: Pop-up settings</string>
    <key>PayloadIdentifier</key>
    <string>uk.co.tomholbrook.Chrome</string>
    <key>PayloadOrganization</key>
    <string></string>
    <key>PayloadRemovalDisallowed</key>
    <true/>
    <key>PayloadScope</key>
    <string>System</string>
    <key>PayloadType</key>
    <string>Configuration</string>
    <key>PayloadUUID</key>
    <string>bceaecbb-e125-42f0-b827-85066b2b01c3</string>
    <key>PayloadVersion</key>
    <integer>1</integer>
</dict>
</plist>

Here's that profile installed in Version 46.0.2490.71:

Thanks gents. Looks promising. I'll give it a go and report back.

This is a lot better than the sledgehammer approach, or managing Chrome via Google for Work, (which involves signing existing employees out and back into Chrome)

Thanks for the config profile.

Works! And doesn't trample existing whitelist (even better).