Ok bare with me I’ll just go over my terminology to hopefully make anything I say a little less fuzzy.
Yeh as you said dealers do not clone keys. For keyless ignitions nobody clones keys, for some makes the backup transponder could be cloned however I’m unaware of any solution that clones a full keyless key. You can get another key programmed in addition to yours by an independent or the dealer (doesn’t require tossing the original).
Nissan rogue I think is x-trail in my market so it’s PCF7953M HITAG AES. Theres some information in the above pdf. But the basics of it are the key has an ID and a seed and response system like you said. When programming a key it’s ID is added to the vehicles white list of accepted keys and the secret key of the car is loaded onto the key (it’s the actual start button on your car that does this on yours).
As you go over, theres 3 elements at play all controlled by the one chip. The proximity part (normally 125khz), the remote part (normally 315/433/868/915 depending on make/model/market) and the backup transponder (again 125khz but much lower power has to be basically touching, this part is actually powered parasitically and not by the key) The remote may well still be a (signed) rolling code as I believe this will only be one way communication. When you get close enough to the to the vehicle you’ll be using the proximity part, when touching the key directly to the button, if the key has no battery for example, then you’re using the passive backup transponder.
Flipper has hardware that would be able to send the remote locking signals, if you knew what to send, but with this likely being some form of rolling code you’ll advance the code kicking out the original at least until it catches up or is resynchronised.
I’ve not really looked at how flipper is doing the RFID implementation but I’d be surprised if it allows us the granular control to emulate the protocol for the transponder in this case
(however some other systems are very similar to more normal RFID tags) and I don’t think it’ll have anything able to do the keyless entry.
Seeing that programming, in the case of your nissan rogue, is done through the passive element/backup transponder of the key I’m not sure how it could be separately programmed as a remote even.
Hope this helps. Any questions on your car/in generally happy to help so fire away.