To avoid .htaccess files of WP installations, affect other WP installations, use the following file system structure:
hosting_account_folder ┌─────┴─────┐ public_html subdomains ┌────┼────┐ sub1 sub2 sub3
In this scenario, mydomain.com points to hosting_account_folder/public_html, sub1.mydomain.com points to hosting_account_folder/subdomains/sub1, sub2.mydomain.com points to hosting_account_folder/subdomains/sub2, and sub3.mydomain.com points to hosting_account_folder/subdomains/sub3.
As you can see, none of WP installations, is a subfolder of any other WP installation.
Note: having a WP installation, as a subfolder of another installation, is not good for SEO, it is a myth. Always use subdomains!