The reason that the updater will work differently on these upgraded devices is that the Flash memory in these devices is smaller, and it there simply isn't enough room for certain upgrades. The noticeable difference will be the lack of Windows Media Player 8.5 and the new Bliss Today Screen will also not be included
Editor's Note
I have successfully performed the update on an iPAQ 3670 which was upgraded to Pocket PC 2002 as well as an iPAQ 3875. I am not experiencing any negative reactions to the upgrade.
There are reports of users attempting to apply this update to devices other than iPAQs. These attempts may be successful, but pdaBlast! strongly recommends against upgrading your device with an End User Update other than the one which is specifically designed for your device.
If you have any questions about the EUU3 release for your specific device contact your manufacturer.