As an example look no further than the Manifold Civil War Battlefields demo. The various layers are not georeferenced with one another. Switch between them and the scales change.
I just tried that and all the layers line up perfectly. Example: pop open the Civil_War_Battles project, double-click the Map to open it, and then the Locations folder in the Project pane, right-click on the Gettysburg location and choose view in Active Window.
It pans and zooms exactly to Gettysburg, with the dot placed right where it should be. There are only three layers, the Battlefields layer, and the two Bing layers in the Map, and they all line up perfectly.
Turn the Bing satellite layer on, and then in the Layers pane set the transparency of the Bing streets layer to 50% and you can see that the two Bing layers are perfectly georegistered... no surprise given that they're both from Bing. Change between layers (you can turn layers off and on either in the Layers pane or by double-clicking the layer tab) and you'll see that does not change the scale.
I get the feeling when you write "layers" you may mean "locations," which are a different thing. As far as I can see, most of the locations have a scale of 1:10,000 but if the author of the project wanted a different scale for some of the locations, say, if the size of the battlefield would be better seen at a different scale, well that's part of the value of locations that you can do that.
I want a satellite image base with 0% transparency overlain by the street map - linework only, no fill so I can see the satellite image and the battlefield points on top. These could be failings of Viewer?? Or do I have to create another file / layer and copy all the components into it? The demo videos all seem to start with the components loaded and the actual setting up process is missing.
All that's easily done, in Viewer as well as 9. Check out the documentation on image servers, as there are thousands of them that can be used, and some of them do, indeed, provide street layers with transparency in between the streets ("Google Maps Street Map (Transparent)," for example).
As for demos, see the many videos on the Videos page and read the introductory books in the documentation. There are hundreds of step by step examples in the Examples book of the user manual. Many of those and a lot of the videos start off from zero.