GameObject with Character Controller Component fails to detect Colliders when its Transform is changed

How to reproduce:
1. Open user attached project "UnityBug_PhysicsIgnoringCollisions.zip"
2. Enter Play Mode
3. Let the game run and observe for about 20 seconds

Expected result: "Character" Game Object always detects Colliders below itself
Actual result: "Character" Game Object does not detect Colliders below itself

Reproducible with: 2019.4.29f1, 2020.3.16f1, 2021.1.17f1, 2021.2.0b7, 2022.1.0a5

Note:

• When the game gets paused, in the Hierarchy window, reenabling active "Chunk" GameObjects resolves the issue for a while, but the issue happens again. Reenabling active "Chunk" Game Objects for the second time fixes the issue entirely and the issue will not reappear for the remainder of the session
• "CharacterControllerTest.cs" contains all the Tranform changing logic