I've been busy in "real live simulator" for a while, so I have only now read all the latest posts. Sorry for the long post but I'm addressing several points mentioned.
sc3 implementation
The sc3 implementation is very limited by definition. I did it because we had the nice Soyuz meshes available and I decided that a VC would be nice. And that lead to a simple SC3 implementation. From that it grew into a more complete project.
I tried to get the correct values for engine performance and weights, BUT I've stated from the start of the development thread that they needed expert attention.
In theory, the 3 docked vessels is no problem, as long as the weights and center of gravity are right for each separate part... In fact, I used the Shenzou addon

as a guideline.
The good thing is that it all can be corrected by editing values in Notepad.
But we NEED the right values and I don't know what they are (and don't have time to figure it out

)
As for going back to a single spacecraft configuration, you already have it before the initial module separation. Just remove the payloads and indicate a single mesh.
Conclusion: I think that the numbers do need to be checked and corrected by an expert. Also, sc3 configuration by attachment points instead of docked vessels is something to explore.
Parachutes, landing and realism / systems simulation
As for the parachute mesh, it's reused from the another addon and intended just to provide some sense of the landing sequence. It is not accurate in any sense.
It is IMPOSSIBLE to have an accurate simulation without programing a custom DLL. Even if I knew how to do it, I wouldn't have time to get any better results than these...
As for the scenarios, I only put in the general available parameters and dates. Salyut orbit might need to be adjusted to fit with the launch dates.
VC and sounds
Regarding the VC, I can improve the MFD integration (angles), specially on the Vizor simulation using camera MFD.
But I can't change the placement, because I'm using a 360º panorama photo. So the pilot must be seated on the place the photo was taken and NOT in the real cosmonaut point of view.
The alternative would be to do a full 3D cockpit mesh. If someone was the time to program it (integration onto a custom .dll so that it is fully functional), I will do it. But for now it's pointless.
As for sounds, it's just the way orbiter handles them. Each spacecraft makes its own sound. So you only hear the rocket if it is selected.
The 7K modules are already configured to play specific sounds, with the filenames matching the files on Sven's site. You just need to convert and put them in the right folder
Suggestions and updates
Your suggestions are noted, and improved configs and situations will be included on a future update. In fact, what we have is a WIP addon, much like a beta version. Perhaps Spacecraft3 to DLL converter might help here.
I'll investigate it, specially because of the EVA capability...