That field ( "Set the sender to the default Joomla email address" ) is referring to the email address set in your global configuration.
Now that you post this problem I realize that is not clear enough. Sorry.

The emails are sent "From" the email address entered in the form. The feature to use the email in global configuration was added only because some servers are not allowing sending emails "from" an address not setup on them.
The main purpose of the extension was to offer a contact form with any feature one might need, so sending emails "from" multiple email addresses seamed useless.
But now I'm considering adding new fields in the profile to set the "from email" and "from name" in a future version.

I'm curious though, why would you need such a feature ?

Michael NInos wrote:

I realize that the the form will send TO the specified email address (support, siteadmin, quotes). But if the user chooses to have a copy sent to himself, the email is delivered as coming from the site's default email address. Also, when replying to a message via the aiContactsSafe messages panel, all of the emails are sent using the site's default email address.

Sorry, but I think you misunderstood the purpose of this extension. It is designed for the visitors of a site to send some information to the administrators/moderators ( or any other destination you might think of ) easy without having to use an email client. The "From" field is normal to be set to the user's email address ( since he is the one sending the message ) and that is the default behavior of the extension, unless you activate the field in the control panel of aiContactSafe ( which was added only because of the limitations set by some email servers ). The "Reply-to" field is set to the user's email address in any case. It will be totally unpractical to be set the a different email address, because if you will hit "Reply" in your email client it will be very inconvenient to have to search for the email address to which to reply.

Michael NInos wrote:

To me, having the option to reply from the messages panel if you cannot resopnd as the individual the message was sent to (support, site admin, quotes) why have the option to reply?

This is like asking if I can't have all the features of an email client why have the email form on the page.
It's a contact form, not a ticketing system. The reply is there for simple replies and you can chose to use it or not.
The filtering of the messages can be very easy done based on the subject of the emails on which you can define your own prefixes for each profile.

Michael NInos wrote:

I appreciate the work you've done and the fact that I haven't had to pay a dime for it. Please don't take offense at my observations.

I am not. I apologize if it seamed that way.
I really appreciate any feed-back I get and I am trying to find the best way to implement the suggestions received.

Michael NInos wrote:

I realize that this isn't a ticketing system but apparently I am not the only one who has missunderstood your intentions with the layout and functions of aiContactSafe.

That is why I've asked how would you use the different "from" emails.
I'm afraid the problem is now that I tried to implement to many suggestions and the extension is getting overcomplicated.
I need to find a balance between "easy to use" and "features rich".

Again, I apologize if my replies seamed offensive. That was not my intention.