1) I was under the impression that a line level signal simply referred to the signal before it was processed by the amp, and not necessarily a specific voltage or whatever you're getting at...
2) Yes the volume is controlled through the PC. If you have a remote knob for your amp, you can use it as well, but that would be kind of pointless.
3) What problems? So far the only question you've asked is whether or not the computer controls the volume, which is does.
4) I have no idea, keep shopping around, my guess is no.
It seems to me like you just don't trust plugging your headphone port into your amp because....well I don't know why. It works just fine, pretty much every single user on these forums does it who doesn't use AUX input, I did it myself for a while before I switched to 5.1. The amp has no problem accepting input from the soundcard's headphone output. Just make sure you set your speaker settings to 2.1 if you're going to wire it that way.
Also I don't know what kind of soundcard you'll be running, but if possible use 5.1, it sounds tons better and isn't any harder to wire.