Short answer, yes, in fact that is the only way I'm aware of programming the remote buttons that are on the FOBIK.
You keep saying FOB, but you're vehicle likely has a FOBIK, there is a difference. Commanders also came with Transponder Keys in the earlier years, and have a remote buttons on the key head of the Transponder key.
A FOB isn't inserted in a key hole or used to turn the ignition switch. It may be as simple as a plastic box on the key chain with remote buttons, it may be as complex as some of the RFID keys used in other Chrysler Models, that you don't have to insert some sort of block to turn the ignition switch, instead press a button on the dash, as long as the RFID FOB is in the vehicle it will start.
The customer key programming feature was removed in 2010 models, and in some Chrysler 2009 models. I "think" the Commander the feature was removed in the 2010 model year. Check your O.M. it will tell you if you have the feature or it will tell you that you need to see your dealer to have duplicate keys made.
Can anyone confirm if the customer key programming feature is still enable on 2009 Commanders?
You will need two valid keys to program additional keys and their remote buttons using the Customer Key Programming feature. You stated you have those.
A couple more things to keep in mind.
*The remote buttons only activate equipment put on the vehicle at the factory. So getting a fobik with additional buttons for more features won't give you those additional options. You have to have the factory installed options for the additional buttons to work. (Yes, we've seen that question posted, someone thinking that all the needed to do to get remote engine start is too get a new key with the button on it, no it doesn't work that way).
*Once a key has been programmed it can never be reprogrammed for another vehicle, i.e. you can't get a used key and reprogram it for your vehicle. You need to get a brand new, never used FOBIK.
*There are several different FOBIK's that work for only some models of Chrysler vehicles, but they all look alike. Make sure you have the right part number FOBIK before purchasing, don't simply go off it looking just like your FOBIK, it might NOT work.
*The key insert is indexed differently than regular keys, so if you try to have the insert cut to an existing key, it will come out screwed up. Some of the key copy machines don't use the index line down the key as an index for cutting it, those can make you a copy. I think if you use an existing insert as the master to copy another insert it should work ok.
*You can get FOBIK's off ebay for as little as $25, as compared to $120 in your link, which the dealer will charge as much as $320-$400 for a blank FOBIK. Buyer beware with ebay, read the bullets above, there are lots of rip-off artists or ignorant sellers that will sell you a used FOBIK or the wrong FOBIK for your vehicle. I would pass on sketchy auctions for one that identifies the exact part number, or identifies which models/year the FOBIK works for, and has a photo of the FOBIK in an unopened factory plastic bag.
*The vehicle has a limit of the total number of keys that can be programmed to it, like 7 or 8. Although I have heard they changed that and the Dealer can now program more keys or reset the vehicle to accept new keys, but I don't know if its true.
*You can also program a much Cheaper POD key, that doesn't have the remote buttons. I have this hidden inside my vehicle, as a spare in case I loose my keys. I have a hide-a-key, but it is just a blade key to open the door (since hide-a-keys can fall off the vehicle) and the more expensive harder to duplicate POD key is hidden inside the vehicle.