I agree, and I think it is the general concensus in the Haiku team. Individual preferences are not going away. We are however trying to merge some of them, as ithas been done for “Input” already (vs separate Mouse, Keyboard, Touchpad, and Joystick prefs). Which is not very different from what Dano was doing, apparently.
A single app also creates more problems in terms of UX design. You have a lot of settings and you will need to put them in separate panels. If you do this by having an entry point icon view, you need to add some way to get back to that after changing some settings. So now your app needs back/forward buttons. If you do it with a tab-like system, you quickly end up with having nested levels of hierarchy (a tabview inside a tabview, or some variation of that). You also need to design ALL preferences so that they use the same window size and all fit nicely in it.
Also, there is often confusion about wether the default/revert buttons will apply only to the “local” settings (the ones shown on screen, and not any hidden part of the UI), the whole settings in the preference app, or something in-between. Or if you don’t do that, you end up re-inventing the window management. Which means you have special not-quite-windows for your preference “cards”, that can’t be stacked and tiled anymore, for example.
So, it was nice when all settings would fit in a single screen like in the early Macintosh System versions. But they gave up on the idea later on, probably for similar reasons.