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.
The "warning" language shown when running
wp rewrite flushshould reflect exactly what did not load themes, or why themes were not loaded:...should change to...
...or...
In the case of WordPress living in its own subdirectory, if
WP_DEFAULT_THEMEis not set, or ifregister_theme_directory()is not called, a wp-cli user may think a step was missed during setup when "themes weren't loaded" is encountered.