I don't know if I understand you question correctly, but maybe I can explain something.
For sending of email, you need a smtp-server. In most cases, only the smtp-server of the provider of your internet connection works: other smtp-server usually doesn't relay the email (there exists something like authenticated smtp, but I leave that out). The smtp-server only is responsible for sending email: the contents are not touched by the smtp-server (except Received-lines, of course).
The sender of an email is given in the email itself as an "Reply To:" or "From:" field. That field is used fom the "From:" field in the receivers email program.
The smtp-server you use and the sender of the email are independent: you can use the smtp-server of account A to send a email using the emailadress of account B*. So that is why those settings are kept in two places.
It is possible to enable a "special transport" to a identity such that a particular smtp-server is used when sending using a particulal identity (you already found that option, as it is the same as in your reply).
*: You can even use a name and email address which is not yours, but a reply isn't received then. However, it is important to know that the name in the From: field is not reliable.