The latter. Just like @hooovahh explained, the files are copied to a temporary location which can result in longer paths.
The output directory for your application determines the location of the temporary folder, which is actually just the name of the executable as a folder (i.e. "Application.exe" but it's a folder).
EDIT: Regarding vi.lib, these files also reside inside the "Application.exe" folder. Here is an example for JSONtext:
"C:\Code\Repository\builds\Untitled Project 1\My Application\Application.exe\1abvi3w\vi.lib\JDP Science\JSONtext\LVClass Serializer"
Here is an example of what it looks like during build.