Thanks Mary.
From that and the comments on the Bootstrap theme issue, it looks like with https://docs.moodle.org/dev/Templates#How_to_I_override_a_template_in_my_theme.3F that the notification files: https://github.com/moodle/moodle/tree/MOODLE_31_STABLE/lib/templates need to be in any custom theme that does not use core Bootstrapbase (Bootstrap V2.3.2). I wonder if the files should really be here: https://github.com/moodle/moodle/tree/MOODLE_31_STABLE/theme/bootstrapbase in a templates folder, like the 'base' theme does: https://github.com/moodle/moodle/tree/MOODLE_31_STABLE/theme/base/templates/core and thus core templates need to be theme independent.