Based on a Github issue I was able to get a collection with Zola taxonomies writing the proper TOML-frontmatter format.

collections:
- ...
  fields: 
  - label: "Taxonomies"
    name: "taxonomies"
    widget: "object"
    fields:
    - { label: "Tags", name: "tags", widget: "list", allow_add: true}

This is written out into the frontmatter as

+++
[taxonomies]
tags = ["tag"]
+++