When the touchpad is set to emulate a mouse scroll wheel while using a circular gesture, swiping clockwise is scroll down and swiping counter clockwise is scroll up. Of course, you can change this if you want:
Steam>Settings>Controller>Pair and Manage>Desktop Layout>Edit>Edit Layout>Trackpads>Left Trackpad Behaviour>[gear icon]>Invert Swipe Direction
Or just swap the "Clockwise Command" and the "Counter Clockwise Command" under Steam>Settings>Controller>Pair and Manage>Desktop Layout>Edit>Edit Layout>Trackpads>Left Trackpad Behaviour
But regardless of the fact that it can be changed, there must be some logic to why the Steam Deck touchpad behaves that way by default, right? Help me make sense of why some dev team at Valve decided that the default should be "clockwise=down" despite these other common scenarios in which "clockwise=up".
It's just a different perspective
Most people that wouldn't use inverted y axis for a mouse or joystick controller would fly a plane with a yoke "inverted". Back goes up, forward goes down.
It's easier to imagine sitting in a plane
Like it's easier to imagine controlling a character on a screen if you were sitting in their head with a plane yoke to control. In that case it would be inverted.
Anyone can learn to use inverted y controls. Just it's not the default everyone learns so it's not "normal"