How do I manage a mix of menu and custom breadcrumbs?
Do I have to create my own Breadcrumb builder class?


Yes, there are many places where you can modify breadcrumbs, but this is the only straightforward way. The custom breadcrumbs should have a priority higher than 1010 (the priority of the breadcrumb builder of Menu Breadcrumbs), so that nodes that follow rules you put in applies() of the BreadCrumbBuilder class can't be controlled by Menu Breadcrumbs.


  How do I set the priority (asked in the comments)?


The priority is set in the service definition, example from the Menu Breadcrumb module:

menu_breadcrumb.services.yml:

services:
  menu_breadcrumb.breadcrumb.default:
    class: Drupal\menu_breadcrumb\MenuBasedBreadcrumbBuilder
    arguments: ['@config.factory', '@menu.active_trail', '@plugin.manager.menu.link', '@router.admin_context', '@title_resolver', '@request_stack', '@language_manager', '@entity_type.manager']
    tags:
      # The priority must be higher than core taxonomy builder (priority: 1002)
      # see https://www.drupal.org/node/1495510
      - { name: breadcrumb_builder, priority: 1010 }


(which is also where you have to look when you want to override an existing breadcrumb builder, you can see here what was considered concerning the taxonomy breadcrumbs)