I haven’t tested this, but if you don’t want to use WP-CLI and ONLY want to use crontab tasks, you would have to add new crontab job for each subsite, like:
curl -s https://example.com/[directory]/wp-cron.php > /dev/null 2>&1
Ref: https://vpsfix.com/7456/setup-proper-cron-jobs-wordpress-multisite-network/
You said your crons are not working for subfolders, but you don’t provide any error messages or explain why it’s not working… however, it should work, if you follow this.
I don’t think you can avoid using wget/curl, unless you write a custom PHP script, you can see this for one example of that:
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