Every PC port faces the same question: should it look like the original game, or like what people remember the original game looking like? OpenGOAL answered with a mix. Several of Jak and Daxter's defaults were deliberately not the console's: its visibility system, its particles and its shadows were all set to the PC's own versions out of the box.
Phaethon answers it the other way. Since September 24th, a game started with no options is the PlayStation 2 game: retail-faithful, with the console's own settings.
Presets, not a pile of switches
Anything beyond the console is a preset you choose in the launcher. Remastered brings the upscaling, the farther detail, the smoother motion and the rest. Speedrun is retail with every setting locked, so a run is always played on the console's terms.
Behind them sits one registry that names every setting exactly once, with its console value and what each preset does with it. A preset is just a named set of values. As of October 16th it holds 200 settings, and 58 of them differ between retail and remastered.
Why it was needed
The launcher used to have an Enhanced checkbox. It was saved faithfully every time a player clicked it, and the game never read it. That was the moment it became clear that settings needed one home both the launcher and the game read from.
Still going
The registry work is still open; not every setting has moved into it yet. The rule it serves is settled: the console's game is the default, and everything else is something you choose.
Alex (maintainer, and a mechanical engineer by trade)