Can RC9800i really control lights via IR? Short answer: Yes.
I have the RC9800i working with my IR dimmer (Lutron MIR-ITFS). But you are correct, you have to remap existing buttons provided to you by the setup of the rest of your system.
In other words, you can't tell the remote what lights you have. After you go through the setup of all of your devices, look at the buttons/pages provided then pick a couple of buttons you can stand not using for its intended purpose.
To remap these buttons go into Settings->Rooms & A/V Devices->Add/Edit A/V Devices. Select the device(s) controlled by the button you want to remap (switching rooms if necessary) then press "Edit" then "IR Codeset" then "Try & Learn"
This gives you a list of function names. Find the function represented by the button you want to remap. Have your Light remote handy, press "Learn" then press the button on the Light remote while pointing it at the RC9800i. Repeat for each button you want to remap.
This works tolerably, but it's not as handy as I would have liked - at least not in my setup. I have a media center PC (running Media Poral but using the Microsoft Media Center remote codes). The only buttons I found convenient are the "Enter" and "Clear" buttons beside the number pad. These appear on page 3/4 of the built-in setup. So the only way I can control the lights is if I'm in an activity that uses the Media Center - and I have to hit the Page button twice, operate the lights, then press Page twice again to get back to page 1. If I ever forget to turn the lights on after I've shutdown the theatre stuff, tough - unless I re-enter the activity which will then, of course, power everything back on.