The idea Glynor is explaining is to have multiple media views of the same stuff.
Correct. You'd have a "management" set of Views and a "normal playback" set of Views. The management Views are usually quite useful to have anyway. The way you use the View to tag files usually doesn't correlate well with the way you want to browse and play files. Having Views tailored to the tasks you want to accomplish while tagging and organizing is quite useful.
The parent of the Playback Views would have a filter that hides all files you want hidden ([Rating] < 2, for example). In fact, if you wanted it to behave something like iTunes, you could easily make an Enabled/Disabled checkbox field, and then use that to filter your Playback views instead.
The User setup suggested by Matt would be easier, but if you want something more flexible, the tools are all there.
One of the core ways that Media Center behaves (and has always behaved) is that when you
Play All on a file, it plays the items visible in the current view (and, assuming Shuffle mode is not enabled, it preserves order). I don't know, and I don't have any power over it, but I don't think this is likely to change. It is deeply rooted in how MC works.
So, what you
cannot do is start playback from a View showing a set of files, and have it ignore some of those files.
Maybe they could add some kind of Playing Now filtering system, but up until now, that is not something JRiver has been interested in doing.