Please check documentation on how to use custom versions: https://docs.directadmin.com/custombuild/upgrading-services.html#override-single-package-version
There is no entry of apache:... in versions.txt, so, it has nothing to override. First column (name until ":") must fully match for an override.
Selection is there already and can be used per-domain. Any subdomain can be added as a domain to get additional features like this, email management and others that subdomains do not have.
If you need DirectAdmin technical support - you may create a ticket about it. To be honest - I'm not yet sure what problem you have :)
Do you mean you have webserver nginx_apache set in CustomBuild configuration (nginx as reverse proxy to apache...
There aren't any limitations for PHP 8.4, you could already switch to alpha update channel, update DirectAdmin and get it installed for a legacy license.