Arbitrary and historical reasons.
A good overview about why and who: https://ahmetburul.medium.com/coordinate-systems-of-3d-applications-guide-ddfa2194ed88
Personally, I'm super annoyed that Z is not up. but that's just me coming from Blender and Unreal. It makes programming 3D games more annoying, imo
Edit to add: With Godot having its origins in 2D, Z is "into the screen". and that orientation basically stuck. Why they used negative, I'm not sure
I know someone who bought a new laptop and complained that the display broke after only a couple weeks
It only showed a super dim display and the viewing angle sucked
I pressed the fancy new "privacy screen" button and it "worked flawlessly" again