Yes this would apply for the commercial product against any others that
are sold. It won't apply against free software because nothing is sold.
Does it really matter? Do you really need to keep the name? If your
fork of the project continues active development while the institute
continues to develop their version then there will definitely be
confused users at some point down the line.
Can't you just change the name and leave this debate in the dust?
I understand that you have put in a lot of effort to get this far but
now you are risking your rep by making a stand on a name that you
didn't originate and therefore shouldn't feel any real attachment to.