When using Symfony DI with autoconfiguration, there is a major discrepancy between equivalent PHP and YAML configs:
If using the YAML config, you can override default options with _instanceof.
If using the PHP config, you can not override default options with registerForAutoconfiguration.

Please note, when I say 'default options', I mean the definition used for ContainerBuilder::registerClasses($definition, $path), as shown in the example here.

The linked project demonstrates this discrepancy by attempting to use _instanceof/registerForAutoconfiguration to make the class ConsoleApplication public.

This appears to happen with any options that are changed from the Definition default values, and can be worked around by calling $definition->setChanges([])