It can be done with shreddit: https://github.com/andrewbanchich/shreddit
It has a built-in option to point it to your extracted GDPR data, and will edit and/or delete all the comments that are listed in there.
Just configure it according to the instructions, and then let it run unattended for a while. It took about 15 hours to delete the 13000 comments on my 12 year old account.
This is correct, most of those scripts can only delete 1000 comments from new/top/controversial.
The method to delete all your comments is as follows:
Do a GDPR request for a copy of your data using: https://www.reddit.com/settings/data-request. Wait until you get the zip file, then extract it somewhere.
Download the free utility shreddit from https://github.com/andrewbanchich/shreddit and point it to the directory where you extracted your GDPR data using the
--gdpr-export-dir
flag.