Not sure about the RF protocol used in these remotes. If you search “arduino Somfy roller shutter” you can find plenty of DIY projects that used Arduino to control these roller shutters. Some of them are completely wired solutions, and some may be wireless (although the few I’ve seen are basically wiring Arduino to the remote buttons, essentially use digital pins to simulate clicking on the remote buttons, and none I’ve seen has decoded the signal yet).
About garage door: we are working (albeit slowly) to finalize OpenGarage (a WiFi-based garage door opener). I can share a few tips I learned about the security code: basically all garage door remotes use some sort of security code (rolling code), so it’s not possible to just sniff and reproduce the RF code to open the garage door. However, many garage door buttons are super simple: just a switch where when you short the two wires it toggles the door. So it’s very easy to use a relay wired in parallel to the garage door button wires, in order to trigger the same action. The only exception is security+ 2.0 (which is the new thing on more recent openers): in this case even the door button has a security chip hence it won’t work by just shorting the two wires. Instead, you can get s security+ 2.0 door button and solder two wires from the button, hence when you short those two wires it simulates a button press.
The more general option is to get a universal garage door remote, solder two wires to the button on the remote, and connect those wires to the relay. Again, shorting the two wires simulates a button click hence triggers the action.