What is the officially recommended way to protect the modified .htaccess files in a composer install from being overwritten later?

[dmitrii-fediuk]

For example, the .htaccess files could be modified (the mod_rewrite section) to setup Magento a into a subdirectory.
What is the officially recommended way to preserve such modifications from being overwritten later?

[maksek]

Please submit question in Magento forum, GitHub only for issue reporting and PR.