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This is a common setup for large organisation and for orgranisation which has country wide branch office. All you need to do register your main domain and subdomain separately, and have MX record separately. Even you can host different mail server for each domain on this scenario.
This is a common setup. Large organizations often use subdomains for non-personal mail types. Servers sending you mail will look for the MX record for the fully qualified domain receiving the mail. Your domain and subdomain are different fully fully qualified domains. You can point your MX record(s) to any hosts that are configured to receive mail for ...
The email service implementation won't treat a domain and subdomain differently. So you will simply need to add relevant MX records for both the domain and subdomain, matching your target mail servers.
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