The "warning" language shown when running wp rewrite flush should reflect exactly what did not load themes, or why themes were not loaded:

Warning: Some rewrite rules may be missing because themes weren't loaded.

...should change to...

Warning: Some rewrite rules may be missing because themes weren't loaded by WP-CLI.

...or...

Warning: Some rewrite rules may be missing because skip-themes is set.

In the case of WordPress living in its own subdirectory, if WP_DEFAULT_THEME is not set, or if register_theme_directory() is not called, a wp-cli user may think a step was missed during setup when "themes weren't loaded" is encountered.