There are also just some things you cannot realistically do in the browser (or over SMS) without having to ship specialised hardware to 18 million people, like reading the NFC chip of your passport. This is needed for DigiD Substantieel and Hoog, which are mandated by the eIDAS regulations.
[1] https://github.com/MinBZK/woo-besluit-broncode-digid-app/
It is also far less likely to be phished, and there is nothing transmitted.
TOTP is the modern WPA2 of security - it's just not good enough when better alternatives exist.