In version 2, layouts are saved with tournaments, in the same way that the Rounds or Prizes are saved with tournaments. Layouts may also be loaded and saved independently from the tournament in the same way you can load and save Rounds templates, or Prizes templates.
In version 3, you may enable or disable the ability to load and save layouts with tournaments. By default, things work the same as in version 2. But you can tell the software that you don't want to save the layout with the tournament. And you can tell the software that you don't want to load layouts with tournaments, or that you want the software to ask you if you want to load the layout when a tournament is loaded.
Here's the thing to keep in mind: when a layout is saved with a tournament, they are saved together, in one file. The layout isn't saved as a separate file.
So, here's another view of the situation I think you are describing:
(1) You start the TD, and create a new tournament, modifying the rounds and prizes, and adding players.
(2) Next you modify the layout a little bit.
(3) You save the tournament as "myTournament.tdt".
(4) You then change the layout just a little bit more, maybe changing the <title> cell (which displays the tournament name) to be in big, red letters.
(5) You save the layout as "myBigRedLetteredLayout.tlo".
(6) You exit the TD.
(7) Later, you start the TD again and load your saved tournament "myTournament.tdt". The TD tells you a layout was saved with the tournament and asks if you want to load the layout as well. You say "yes".
(8 ) You check out the layout and notice that the <title> cell isn't in big, red letters. What gives?
In step 3, you saved the tournament and the layout was saved with it, all in one file. In step 5, you saved the layout in its own file (like a Rounds template). The tournament file saved in step 3 does not "reference" the layout saved in step 5, it has a complete copy of the layout saved with it. But that copy was saved before you made the change in step 4.
Clear as mud?