You must have an RF interface to communicate with your skylights and unless you are an official partner I doubt that you can obtain all necessary information to build one specially for the Pi.
Also it does not seem to be an ordinary wireless communication technology.
Two-way radio communication complying with the EN 300-220 standard
The io-homecontrol® protocol handles two-way radio communication at
frequencies from 868 MHz to 870 MHz. It complies with the EN 300-220
standard for low-power radio applications.
So you either hook up the remote control to the Raspberry. (IMO those relays are quite overkill, some simple transistor can be used to do the switching instead, so the additional hardware would not be so large.)
Or you can buy a TaHoma® box for centralised control and management of the house from a smartphone, tablet or computer connected to the internet. As I understand, it is basically a gateway for io-homecontrol. You only have to connect the Raspberry Pi to the internet to be able to control your lights indirectly.
It is more expensive but you do not have to hack a remote control.