You can control the password recovery because it uses the system.net.mailsettings section so whatever you put there will be used for password recovery.
Currently the from address not so granular per feature and it sends most messages using the site settings from address. It would not be too difficult to add settings in each feature that can send mail though so I will keep this in mind for an upgrade.
Currently the web store uses its own from address so I can have it mailed from email@example.com
However, it is important to note that if the from address is not the same as the smtp user it can make the mail appear as spam. Its ok if the email addresses used are all from the same domain as the smtp user or aliases of the same account. Basically some mail systems will do a reverse DNS lookup on the smtp server and if the domain on the mx record for the mail server doesn't match the from address the mail can be flagged as spam. So if you are sending from your own smtp server you want to make sure there exists mx records for your domains that resolve to the same ip as the smtp server.
I don't think we want to have per feature smtp settings, that would be cumbersome and complex. I could add the additional from addresses, but it also can lead people to use different addresses that don't correspond to the smtp account, so there are some tradeoffs.