However that means that after you reply, your original e-mailaddress is visible. In which case there is no advantage to using an alias over simply using [[Special:EmailUser]], which is effectively also an alias for the first mail.
Not at all. You can send mail from any address you choose; which is why, when you send mail, your email provider will recommend you use SMTP servers (POP/IMAP are used to retrieve mail - SMTP is the transfer mechanism) provided by your ISP.
For example my work email is tom@<work address>.com, but my email client connects out to BT's SMTP servers.
This is why email spoofing is so such a problem - there is nothing actually stopping me from sending email as krinkle@gmail.org so long as I can find an SMTP server that will accept my mail. Much of this is filtered out at the other end (by the receiving server, who calculates whether the mail is genuine or not).
Long story short is: if @users.wikipedia.org was set up as an alias then you could use it to send mail - in Gmail it is as simple as adding it in settings as one of your sender addresses, then waiting for a confirmation email to arrive (and click accept).
FWIW my 2p is that it would be handy for me when negotiating with people for images/content release - or continuing OTRS contact outside of OTRS - to have a Wikipedia address.
My thought is that it should be tied to Special:Emailuser. If you have that turned on (and maybe a special EmailAlias right, or other level of control) <username>@users.wikipedia.org aliases to your email address. (I'm trying to apply a level of KISS here).
Tom