Bumping this as I haven't found any resolution in the matter.

That's handle with something known as LaunchServices. Each account has a plist, com.apple.LaunchServices.plist in the home account's /Library/Preferences/ folder that stores LSHandlers for document types.

I don't have the full Acrobat on my Mac, but when I change PDFs to open in Reader and entry like this is added to my com.apple.LaunchServices.plist file-

<dict>

    <key>LSHandlerContentType</key>

    <string>com.adobe.pdf</string>

    <key>LSHandlerIgnoreCreator</key>

    <true/>

    <key>LSHandlerRoleAll</key>

    <string>com.adobe.reader</string>

</dict>

This is stored inside an LSHandlers array-

<key>LSHandlers</key>

    <array>

        <dict>

            <key>LSHandlerContentType</key>

            <string>com.adobe.pdf</string>

            <key>LSHandlerIgnoreCreator</key>

            <true/>

            <key>LSHandlerRoleAll</key>

            <string>com.adobe.reader</string>

        </dict>

    </array>

You can probably use that as a template with a custom MCX but change the identifier from com.adobe.reader to something like com.adobe.acrobat.

But the best thing would be to make the same changes on a Mac with Acrobat installed manually and examine the plist file. Then you'd have to add it in the appropriate settings to a Managed Preference or perhaps a Config Profile with a custom payload.

hope that gets you started in the right direction.

http://duti.org/documentation.html

+1 for duti

Then;

duti -s com.adobe.Acrobat.Pro pdf all

+ 2 duti