There are two factors that control this.
If you go to Settings->Identities, there is a setting easy to miss Compose new messages from ...
In addition to the above, there is a fantastic feature available for those who want to completely isolate categories of email from each other. If you go to Settings->Folders and click Edit next to a folder, and ensure you have Show advanced preferences set, there is a Default identity associated with the Folder. This controls the Identity that will be used when you reply to a message in that folder, or compose a new message while browsing that folder. By setting this on a Folder and its subfolders, you can create a sort of sub account where you are unlikely to use the wrong Identity by accident.
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