So...this is my question. Is it by design that mail coming from one of my <virtualdomains.com> is sent from <servername.hostingbox.net>?It's by law. ;-)
Postfix calls itself by the name of the server it runs on. Always. This is the only sane way to do it, because a large number of recipients base their trust on reputation. If your sending name changed for every message they would have to be suspicious. The idea is that your server sends out messages using it's One True Name.
Add in reverse resolution, SPF and/or DKIM, and respect for RFCs, and you have a recipe for always getting your messages through. Start screwing around with how your server looks, and the big guys aren't going to want any truck with your mail.
If mail is sent to myuser@virtualdomain.com which is hosted on my servername.hostingbox.net, the reply or sent mails appear to come from servername.hostingbox.net. I was expecting it to show either mail.virtualdomain.com or virtualdomain.com?Oh, wait...You're talking about the From: field or the Received-From: field? Now I'm confused. ;-)
If the From field is wrong, this would be a client issue. You haven't told us what webmail client you're using to get this result. Configuring Usermin to use the right address is documented here:
http://www.virtualmin.com/component/option,com_openwiki/Itemid,48/id,email_troubleshooting/
#usermin_webmail_sends_with_incorrect_fromaddress