Lenovo/IBM didnt really consider the case of FDE when they invented R&R - in fact, all the R&R products are fairly/completely incompatible with FDE at a low level. Think about it - they take over the booting of the machine, assume they can write to the user data area, assume they will work without any authentication etc. All bad things.
Lucky for you there is indeed a plugin for R&R which adds EEPC encryption support to it. I'm not sure its publically available yet though. You probably need to discuss getting it from your account manager.
Isn't that the optional SafeBoot fileset for IBM Rapid Restore? I know it was there in version 4x. The potential problem with that, is that a user could restore their computer to an unencrypted state and "forget" to reinstall SafeBoot. We keep our reimage baseline to include only OS and software distribution component (SMS, Radia, whatever...). The user has to connect to the software distribution system to get their critical apps (Office, business apps, AV, and of course... SafeBoot). Since we had SafeBoot before it was purchased by McAfee, we have not yet implemented ePO. It could be considered somewhat safe, if ePO was included in the Rapid Restore image. That way you could push down AV and SafeBoot to the client.
If you give users a choice, they will chose to not encrypt because they don't see the value in it. They only see that it puts an extra barrier between them and what they want to accomplish. Most users just want a magical notepad never fails them and does everything they want (even when they don't know what that is).
Same kind of thing - you need the EEPC v5 version though. It's not commonly requested so I don't think it's generally available. Most people seem to find RR incompatible with their business needs, I guess for many of the reasons you've already found.