Dear Rabbi Lewis, Thank you very much for taking the time to answer my question. I have a follow-up question: *Why* does Rav Kook write that it is lechatchila to use one’s traditional script? Is it a Torah law, rabbinic law or some other consideration that makes it lechatchila to use one’s traditional script and only bedieved to use a non-traditional script. It seems to mean that by not using one’s own Mesorah the quality of the Mitzvah of Tefillin falls to the low level of being merely bedieved. Thanks again for your time and effort.

The reason brought by Rav Kook is the Pasuk in Mishlei "Al Titosh Torat Imecha" – don't forsake your family tradition. This is brought by the Talmud [Chulin 93: et al] as a source to stick with our family traditions even if they have no written proof. It is brought by various Halachic sources in the same context as well [e.g. Kitzur Shulchan Aruch 158:1]