To reproduce:
1. Open the project that i attached "animatePhysicsBug.zip".
2. Open "Main" scene and enter Playmode.
3. Observe the scene.
4. Notice that platform on the right is not applying any physics to the rigid body sitting on top of it.

There are 3 platforms, with identical cubes on top.
Platform on the left uses Legacy Animation. (Animate physics checked, rigidbody Is Kinematic checked)
Platform on the right uses Animator. (Update mode set to Animate Physics, rigidbody Is Kinematic checked)
Platform in the middle is the one which is moved by the code and not animation (by default it is using transform.position and acts like platform on the right, if you press button in game window it starts using "Rigidbody.MovePosition" and starts acting like the platform on the left).

Expected result: Platforms with Legacy "Animation" and with "Animator" apply physics (velocity and friction) to the rigid body sitting on top of it.

Actual result: Only the platform with Legacy "Animator" applies physics. Platform with "Animator" acts the same with "Update Mode" set to "Normal" and "Animate Physics", and applies no physics to the rigid body sitting on top of it.

Reproducible with: 5.2.3f1, 5.3.6f1, 5.4.2f2, 5.5.0b11, 5.6.0a2