Indeed. It looks like even the non-hierarchical pages get breadcrumbs. Thanks for pointing that out.
To add breadcrumbs into the Custom Navigation Menu Items, you would modify or override this template (within lib/pkp):
Given that most other public facing pages have breadcrumbs, this might be a good thing to pull request back into the core code.
Similarly, the template for Static Pages is here (within plugins/generic/staticPages):
Almost certainly the generic breadcrumb template, which you identified earlier, would be the most appropriate for these, but you would use the currentTitle parameter, rather than currentTitleKey:
{include file="frontend/components/breadcrumbs.tpl" currentTitle="$title"}
Conveniently, the variable $title is used for the translated page title in each calling template.