Alternatively, a complete recipe (without referring to directories
that I definitely don't have here) to reproduce the problem could
answer all those questions succinctly and efficiently.

Here it is

1. cd /tmp

2. git clone git://git.sv.gnu.org/emacs/org-mode.git

3. cd org-mode

4. make autoloads

5. Create /tmp/bug.el with the following contents:

-----

(add-to-list 'load-path "/tmp/org-mode/lisp")
(require 'org)

-----

6. Create /tmp/bug.org with the following contents:

-----

* TODO start clock on this test item

-----

7. emacs -Q /tmp/bug.el

8. M-x eval-buffer

9. C-x C-f /tmp/bug.org

10. Observe error in echo area

Note that doing emacs -Q -l /tmp/bug.el in step 7 does _not_ trigger the error.

Best,

Ihor