The working mode mentions normative and non-normative issues. However, there is a whole range of issues that falls a bit between the cracks, which is when the web-exposed API of a feature is outside WHATWG, but requires some "hooks" into a WHATWG spec.
A good example for this is the update the visibility state steps, where the HTML spec calls algorithms in several W3C APIs, which might be in different stages of maturity.
https://github.com/whatwg/dom/pull/1462 is a current in-flight example (at the time of publishing this OP), where the processing model is in DOM but the API is exposed in a W3C spec.
I think the working mode should be explicit about how to treat this type of change, as the current process around this seems inconsistent.