The extender also comes with wired emitters, which can be attached to the IR receiver of your devices if there is no room in front of them for the "blaster".
I would be surprised if the 1000 didn't come with the extender in the box...the 890 comes with it included so I assume the 1000 would be the same.
As for the "discrete RF codes for lights etc" question, I suggest reading remoteshoppe's reply more carefully. You CANNOT control RF devices directly. This is the case for ALL RF universal remotes. They can only control IR devices via their extender.
The only exceptions to this are that Harmonys will supposedly directly control RF devices that use the Z-Wave protocol. However, I don't think it has been implemented yet...should be in a future firmware upgrade. Also, very few devices(yet) use the Z-Wave protocol. You might find it hard to find one compatible...I wouldn't count on your lights being one of them.
Some people have been able to directly control X10 stuff using UK model Prontos, although I think it's classed as a "hack" and isn't easy to do, orvery reliable. Also, it only works for UK Prontos with UK X10.