Sooooooo... I just had to install a toilet in our unfinished basement :-)
First I installed drywall on one side of the wall to give a bit of privacy.
Then I turned off the water to the house and cut down the copper pipe, before installing the compression stop value for the water supply line.
Then I used 3/4'' treated wood to mimic a finished floor cutting a hole around the drain and then cutting the drain pipe down flush with the wood.