Assume your email address is "email@example.com" and your other email address is "firstname.lastname@example.org."
When you setup an email account on your iPhone, you tell it which account you want to to use to log in and send/receive email.
You can change the "From:" line to be anything you want (using the "comma trick" on iOS or other settings in other mail clients), but Google does not want you to be able to "spoof" your email address without making it clear which account it came from. The reasons for this should be obvious.
When you send email, you connect to a SMTP server and give your username and password. if that username is "email@example.com" and the "From:" line is "firstname.lastname@example.org" then Gmail will automatically add the "Sender:" header which contains your actual Gmail address. (Outlook displays this as "via" I believe.)
The only way to avoid that is to have the username that you log in with be "email@example.com" rather than "firstname.lastname@example.org".
The easiest way to do that is to use Google Apps for your domain which is free for up to 10 users.
You can still set that up as a "Gmail" account in iOS, but when you send email it will not have the Sender: header added because you are sending from the same account that you use to log in.
The only drawback is that you will have two accounts now in the iOS Mail app, which is (I assume) what you wanted to avoid by using the comma trick in the first place. You'll have to decide which is more important: having one email account in iOS (and having "via"/Sender: header added), or not having Sender: added and having more than one email account.)