The multicol spec doesn't define the interaction between 'column-fill' and elements that have 'column-span'. The definition of column-span says:

Content in the normal flow that appears before the element is automatically balanced across all columns before the element appears.

I think it's reasonably clear that in a non-paged context, this means that column-fill is only honored in the part of the multicol after the last column-span: all element inside it. However, it's less clear what happens in paged media. Reading the text quoted above literally, the spec currently says that column-fill: balance-all behavior (rather than balance, which is the initial value) is required on any pages of a multicolumn element where a later page has a column-spanning element.

This should actually be defined in a somewhat formal manner. The current spec appears to be more of a use cases document than a specification on this topic.

/cc @neerjapancholi