You asked several questions about the privacy of Gedmatch:

"#2. How private is your entire genome once you send it to this site? Who sees it? How is it shared, or how can it be shared? Is your "real name" ever published in any way related to your genetic information? How is your privacy potential violated, if at all?"

While it is true that you have to send your whole raw data file to GedMatch, no one else can access your raw data file. So that is private. It is only there on the servers so the computers can run the matching reports when asked to by a user.

Anyone can see anyone else's match lists. If you know a kit number, any kit number, you can run certain reports with it. But all they will learn is who is and is not related to a kit. They do not have access to your raw data. I think they can use the ethnicity reports, but am not certain. (I ignore those because they are basically pseudo-science at this point and not worth my time or effort).

Plenty of people do not use their real name with their kit number. You do need to provide that upon signing up for the site, but you can always choose to have something else displayed. Or nothing at all if that is your wish. Same with email addresses. But I will tell you that not listing anything defeats the purpose of people trying to contact you because they are a close genetic match. People who do not list an email contact at all go in my "I have too much other stuff to do and so I will not bother with this person because they are more concerned about taking information than sharing it." My opinion. But when that person is also the one with the largest segment match -- its frustrating.

I administer my kit, and that of 4 relatives. All of the kits are associated with my login, and have my email address as the contact. But for the name of my relatives I use their first initial and their last name, and then add the info that I am the contact person. For example:
S. Hadley (contact is Elizabeth Ernst)

You can choose to upload a Gedcom or not. Gedcoms are searchable -- but not easily. You can choose to put in YDNA or mtDNA haplotype info if you want -- or not. Basically, you choose the level at which you are comfortable with sharing information. You can always start with the least amount of "viewable" info -- no user name, no email, no Gedcom, no extra information -- and open up as you want. But understand that if you do not give people a way to contact you then they wont -- and you risk losing out to contacts who can help you.

(And if you have a private tree on Ancestry, or no tree at all linked to your DNA test -- I guarantee you that the vast majority of your AncestryDNA contacts have "culled" you from their working lists. Too many takers out there and not enough sharers.)

Hope this helps,
Elizabeth