For constructive feedback - I got the feeling from the codebase that it's a bit too opinionated for my use case. Aside from idiosyncratic naming (use of constant case, or folders starting with underscore) and formatting (inconsistent indentation), I think the template could benefit from using common building blocks already available in the ecosystem, rather than every aspect being custom made.
There are common libraries and patterns that are "idiomatic" in Node.js (or any other language ecosystem for that matter), and most boilerplate projects consist of a curated selection and combination of such common building blocks.
For example, Handlebars or EJS are typical solutions for templates. (More typically these days, React rendered server-side.) Mocha, Jest, Ava are often used for testing. There are popular modules for JSON document database.
A big advantage of using "community standard" libraries is that each project becomes more consistent and predictable, in organization/structure and how features work together. Having each module developed, documented, and maintained by the wider community is more efficient too, so that we can all benefit from - and contribute to - the open-source ecosystem.