I am asking due to new changes in their billing for webflow by Dec 31, or has that feature been removed?
However you want. Invoice them through your regular invoicing system. If you want automatic, recurring billing to a customer’s credit card, you can probably to Xero, MYOB, even vanilla stripe.
If you read the press releases, Webflow recommends Bonsai, however it has issues for many in non-US regions, where taxation follows different rules.