So I'm late to the party as usual. I want to make one point here - only because the OP is leaning toward an RF base station remote control solution. IF you put in an IR/RF base station, you do not need an ir-routing matrix switcher - it will be redundant. WIth the right level of URC products (and I'm sure others) you can assign ports to the devices in the IR setup - so the base station/remote configuration IS your IR routing - e.g., you have 2 of the same DVR. In your remote programming, you designate that DVR 1 commands only trigger IR through port 1, and you designate DVR 2 commands trigger IR only through port 4 (or 2, 3, 5, or 6). Run your IR emitters from the ports to each of the DVR's and you're good to go (you may have to cover the IR buds with a shield to prevent cross talk if the other DVR is right next to the first one). This is how mine is setup currently. My switcher is just that - a dumb switcher (well, ok, it's got the capability, but I had the URC setup before the switcher). The URC base station routes all of the IR codes to the specific devices by port (assuming you configure it to do that). If you're dead set on the IR/RF base station setup anyway, might as well save some money on the switcher.
Talk to an authorized dealer and see if he's willing to provide the software if you purchase the remote equipment from him. Hopefully he can, if not, talk to other URC dealers in the area. Depending on what model remote you get and assuming you get the software, yes, you can program it to do what you want. I have programmed my MX3000 and MX980's myself, even teaching my dealer a few tricks in the process. The problem I have with iRule and others, is that I really LOVE a hard-button remote for just about everything a/v related in terms of transport/control functions. My first remote was the MX3000 touchscreens, which only has hard buttons for volume and channel (and mute, I think). That was a PITA to use for dvr and dvd playback. Since I've gotten two 980's, the 3000 is retired and is sitting in the "for ebay" pile.