In our case, as you can see in the samples we are uploading to the
Github, we follow the first option exposed by movra: create a Blend project and the directory structure there (BlendProject/Assets/...). As Blend does not allow you to add existing folders to the project, all the files and directories are always created from Blend. And then you can open the Unity project by selecting the BlendProject directory.
I tried that extensively with Visual Studio (not Blend). Either Unity complains that the directory already exists when you try to create it, OR Visual Studio complains that the directory already exists ... it's a chicken and egg situation.
If you VERY carefully look at the beginner tutorial, there are some shenanigans behind the scenes. You carefully indicate that Blend "has to" create the Assets folder - yet, if Blend created the assets folder, why was there a Unity icon at the desktop already? Also, in the video, Unity showed a recently opened project instead of "Create." How did it know there was a Blend project there and that we wanted to open it as a Unity app? I don't think what the video showed was what actually happened.
That's why I posted about the workflow docs. From a person trying to learn Noesis, it's rough. I got it working for a glorius one edit cycle, then Unity refused to open the project. Not quite sure what I did. I later recreated the two projects 4-5 times trying different versions of the chicken and egg

including 'create the solution,' different names, which was first and which was second, etc.
I eventually settled on creating a completely different Visual Studio project and using "Add existing item" and then using the drop down on the "add" button to link. I am getting errors with Noesis namespaces, haven't quite figured that out yet. I may have to edit visually with one file and manually paste in the XAML, which is really messy.
Starting to wonder if it's worth it, especially as I have to render into a texture for my VR assets. Might as well just use a bit-mapped GUI anyway. No real advantage to Noesis at that point. (sorry, not trying to be rude, just working through my options).
== John ==