Curious, WordPress shows that both the top level terms have records directly associated with them. Other than a malformed data structure when WordPress is retrieving terms, I cannot think of any programmatic way only some of the lowest level terms would be excluded if the top level terms are excluded.
As I am not using these two terms, for the incorrectly showing branches, I flattened the hierarchy and moved the root of these branches to the top level. All the lowest level terms now show as expected. The taxonomy has a weird structure now, but it works.
Related, is there any progress on the new styling of the filters? I implemented your solution for an options drop down to change the results sort order. It works well, but getting the styling of the drop down to be the same as the other filters took longer than implementing it.