You can change the volume of an entire audio clip with the mouse, using the central white handle at the upper end of the clip.
This should answer one of your concern. This volume change is dedicated to the audio clip.
You can as well draw a volume envelope on the audio clip, using the pencil tool. This still is internal to the audio clip and is a complement to the global level of the clip fixed with the white handle.
You can see that Nuendo did start to implement an object oriented clip, in the futur we can hope to see more (SB did talk about that in a blog according to another user), like the possibility to add EQ and effects to a clip, independently from the track settings. Then we’ll have the power of Samplitude and Sequoia inside Nuendo.
You could as well define a track volume for the entire track, using the function “create initial parameter event” in the automation panel (F6). Just select your initial volume with the fader and select this function.
This will put the same volume on all the track, so that when you are in automation read on this track, the level cannot be accidentally changed. This initial volume will be used as well when punching out from an automation pass, if you are not using the “virgin territory” option. For music i prefer the classical non virgin territory method. I’m not used to virgin territory, but this is certainly interesting for post.
Nuendo is very powerful concerning the automation. You have about the same power and functions (and even more thanks to the screen editing possibility) than on the largest analog consoles of the eighties. If you read the manual a bit, you will discover that impressive automation power.