Well this is a tricky situation... they are "internal" to your org, but "external" to the suite....
As it stands on your current implementation, I don't think listing all your domains as internal is in your best interest at this time.... it's not helping with the bounce situation (which is a calculated metric based the individual suite and how many hits were recorded), and since each report suite is fully separate, you really can't see how the traffic is moving between domains....
I am not sure what your network looks like, but one consideration (but it's a lot of work, and may or may not work for you), would be to migrate all your sites into one global tracking suite (using Virtual Report Suites for each domain).
I've done this in our org, tracking 30 sites, 3 mobile apps, and "extended content subdomains for the 30 sites) all into one global tracking suite... I then have virtual suites for each "core site", "app", "all apps together", "extended content X together", "extended content Y together", and "core + app" and "core + app + extended", etc.
Then all those domains are treated as internal URLs, I don't get bounces when someone enters on site a and goes to site b, and I can look at the pathing between sites using a the flow diagram or creating segments that look for specific sequences.
But this is a lot of work, and a lot of planning, and as I said, without understanding your needs, I don't know if this will work for you, but it is something you might want to investigate.