The script at admin/tool/uploadcourse/cli/uploadcourse.php always creates new courses in the Topics format instead of respecting the default setting under Site Admin > Courses > Default course settings.

To replicate:

Go to yoursite.com/admin/settings.php?section=coursesettings and change the Format to Weekly (or anything else besides Topics)

Create a simple course upload CSV file, I used:

shortname,fullname,category

Weekly Course, Weekly Course, 1

Go to Site Admin > Courses > Upload Courses and upload the file in create mode. Note the course defaults are populated into the UI under the "Default Course Values' heading 

Create the course and verify it is weekly format.

Delete the course.

Access your site root via SSH and run the script in createnew mode or createorupdate mode with update mode allowing defaults

sudo -u www-data php /var/www/html/moodle40/admin/tool/uploadcourse/cli/uploadcourse.php --mode=createnew --file=/home/ben/courseupload.csv

Observe the course is in Topics format