the full installer provides an identical setup as the sinlge installs. If you have a running gotm setup, the full installer will not give you anything different.
I haven't heard about problems with indistinguishable civ colours in the gotm mod scenario.Every civ gets a default colour and a 2nd colour as preset in case the first is used in a game by another tribe as default. For example, when Rome is in the game, Babylon is blue, without Rome Babylon is red. I would think there are some crossed settings (a default colour of a civ is another one's extra colour) so that with certain combinations of civs there are some colours used twice. I will have a look at it, but it will probably need another update for the gotm_mod.nic scenario file to change that.
Scenario updates will still be posted in this thread. Right now, the full installer just give you what is already available. It's advantage lies in the much easier installation: it needs one installer to be dl'ed, one installer to be executed. That's all. It's very useful for newcomers and when a re-install is to be done, e.g. because of a re-installation of Windows which happens frequently to Win-users, as you might know.