Reproduction steps:
1. Open the attached “UIToolkitSortOrderBug.zip“ project
2. Open the “Assets/Scenes/SampleScene 2.unity“ Scene
3. Enter the Play Mode
4. Observe the Game View

Expected result: The green document is on top of all the documents
Actual result: The green document is obscured by the light blue, yellow, and green documents

Reproducible with: 6000.1.3f1, 6000.1.16f1, 6000.2.5f1, 6000.3.0b2
Not reproducible with: 6000.0.58f1, 6000.1.2f1,

Reproducible on: M1 Max MacOS 15.5 (Tested by CQA)
Not reproducible on: No other environment tested

Note: The user mentioned that the issue is reproducible in the 'SampleScene 1.unity' Scene, however, I was not able to confirm this behaviour. Reproduction in the 2nd scene seems consistent.