I didn't include any steam libraries with X3R, so it's clean unless valve modifies the binary when it's uploaded. I haven't tested how the downloaded version yields to copy and pasting, try asking here http://forum.egosoft.com/viewtopic.php?t=332472 and if no one answers I'll check it.
TC and AP do include steam functionality so I'm not sure how it'll look there. Egosoft has a general policy of removing any copyprotection a year after release, though don't quote me on that I didn't get to look into TC and AP too much yet (hell I don't know most of R still, it's a non-trivial amount of code;p).
And yeah TC and AP are generally scheduled after R, so unless I get fired or some serious issues come up expect those after R is finished.