Thank you Gustavo, I got this to work after revisiting!

I changed my org-agenda-files to a single variable "org-agenda-files.org" , and populated 
the file with my agenda files.

I modified the wrapper script to call the (org-agenda-files) function.

This is so nice - I have a lot of org-mode files and the ability to remove 
files "root" heading is really nice when filtering by tag.

#+begin_src emacs-lisp
(defun njn-org-refile-filter-targets (orig-fun &rest args)
  (let ((targets (apply orig-fun args))
        (agenda-files (mapcar #'file-name-nondirectory (org-agenda-files))))
    (cl-remove-if (lambda (x)
                    (member (car x) agenda-files)) targets)))

#+end_src


On Sat, Nov 2, 2019 at 8:06 AM Gustavo Barros <gusbrs.2016@gmail.com> wrote:
Hi Nate,

On Fri, Nov 01 2019, Nathan Neff wrote:

> Indeed, I do use org-refile-use-outline-path 'file.  However, I have a
> simple
> directory specified for my org-agenda-files.  ("~/org-mode")
> Therefore
> I'll need to
> do something a bit different.
>
> It appears that your solution creates "targets" which is the targets
> list
> of course, and
> then it creates "agenda-files" which goes through org-agenda-files and
> finds all the filenames
> in org-agenda files.
>
> It then mutates "targets", and removes any entry which is a filename
> from
> org-agenda-files.
>
> Since my org-agenda-files is simply ("~/org-mode/") none of the
> entries
> match.
>
> Hmmm, let me ask:  Why not simply go through targets and remove any
> entry
> whose value is
> a simple filename?  Why search org-agenda-files first?  This function
> also
> assumes that the org-refile-targets
> always comes from org-agenda-files.
>
> I'll play with your function and see what I can get -- thank you for
> the
> head-start!
>
> Thanks
> --Nate

I'm glad this might be useful to you.  And you are correct in all of
observations.

My main point is simply that, as things stand, you won't be able to trim
the file level candidates with `org-refile-target-verify-function`, as
they are hardcoded.  But this simple function is the sketch of a
(hackish) way.

`org-refile-get-targets`' main purpose is to return the list of
targets. The advice function grabs this return value, filters the list
and returns the filtered list.  How it filters may depend, as you noted.
I've chosen a simple criterion which meets my use case
(`org-agenda-files`, as I specify the individual files directly there,
and use only those as refile targets).  Indeed, it does make some
presumptions, as you noted.  (The function does not "search
org-agenda-files" though, it just gets the list of their names, which is
contained in the variable).  In your case, you will certainly have to
devise another filtering criterion.  I think the one you suggest is a
good one too.

Best regards,
Gustavo.