The crux of the issue is in projectile.el.

In this function:

;;;; Find directory in project functionality
(defun projectile--find-dir (invalidate-cache &optional dired-variant)
  "Jump to a project's directory using completion.

With INVALIDATE-CACHE invalidates the cache first.  With DIRED-VARIANT set to a
defun, use that instead of `dired'.  A typical example of such a defun would be
`dired-other-window' or `dired-other-frame'"
  (projectile-maybe-invalidate-cache invalidate-cache)
  (let* ((project (projectile-ensure-project (projectile-project-root)))
         (dir (projectile-complete-dir project))
         (dired-v (or dired-variant #'dired)))
    (funcall dired-v (expand-file-name dir project))
    (run-hooks 'projectile-find-dir-hook)))

projectile-complete-dir eventually calls projectile-project-dirs, which does the following:

(defun projectile-project-dirs (project)
  "Return a list of dirs for PROJECT."
  (delete-dups
   (delq nil
         (mapcar #'file-name-directory
                 (projectile-project-files project)))))

As you can see, it's simply listing all the projectile tracked files in the project and slicing off the file name from the path, leaving us with the directory path. This misses out on directories which only have directories as children.

I'm working on hacking this up on my local copy, but it's inelegant and doesn't take advantage of projectile's caching. I will likely substitute this for #'file-name-directory and flatten the whole list. I can help with this issue as well, I just don't know the best way to go about it as there are multiple routes. My hack would likely be untenable for large projects.

(defun get-dirs-from-path (path)
  (let ((directories '()))
        (while (not (or (equal path "/") (equal path "~")))
          (setq path (file-name-directory (directory-file-name path)))
          (message "path: %s" path)
          (nconc directories 'path)
          )
        )
)

I'm working on hacking this up on my local copy, but it's inelegant and doesn't take advantage of projectile's caching. I will likely substitute this for #'file-name-directory and flatten the whole list. I can help with this issue as well, I just don't know the best way to go about it as there are multiple routes. My hack would likely be untenable for large projects.

(defun get-dirs-from-path (path)
  (let ((directories '()))
        (while (not (or (equal path "/") (equal path "~")))
          (setq path (file-name-directory (directory-file-name path)))
          (message "path: %s" path)
          (nconc directories 'path)
          )
        )
)

I just realized this won't work, as it'll go all the way up to the root of the fs. You'd need to pass in the project path and go up to that as the root. Either way, you'd almost certainly want to look top down