These modules -- are they related or dependent to each other? Are they of the same module type -- ie. magento2-theme, magento2-module, magento2-language?
Do you have your vendor name configured in Magento Company profile?
If all these are yes, then put the modules within a directory that matches your vendor name:
Here is good documentation on composer directory structure, naming, magento package types, etc..: https://devdocs.magento.com/guides/v2.3/extension-dev-guide/build/composer-integration.html
Documentation for extension repository structure: https://devdocs.magento.com/guides/v2.3/extension-dev-guide/prepare/ext-repo-structure.html
I'm wondering if
validate_m2_package.php is old and has not been updated to support the multiple package structure. The last update was in April 2017 on this validation tool.