Yes, this is something you’ll do in the Rails console, and the topics you linked to provide good guidance.
However, before you go on, please consider that you’re actively changing settings for all users, possibly against their (manually configured) intentions. A less intrusive alternative would be to only change the defaults (as you did already, at least for mailing list mode), not touch existing users, and write a post that explains to them how they can configure the amount of mail they get themselves.
If you decide to go ahead with changing user settings, I’d recommend that you make sure that you only reduce the amount of mails that users get. For example, disabling mailing list mode but setting a category to Watching for all users is not safe in this regard: What if the user already disabled mailing list mode intentionally? Instead, I’d recommend that you filter for the list of users that still have mailing list mode on, and only for them disable mailing list mode and watch a category instead. After that, I’d write a post explaining what settings you changed, what that means for your users and how they can revert if they liked the old way.