OK, so try this:
Create an Advenced 3D comp and set an Essential Property (in my case, a color)
Nest this comp in a new A3D comp multiples times.
Collapse transformations on all these layers.
Change the color-EP for all these layers.
So far, everything works.
Now, turn on the 3d switch for all these layers.
Boom - all EP's are cancelled and set to the same value.
I have tested and confirmed that it works as expected in Classic 3D.
So the bug is in Advanced 3D.
See screenshots
After Effects 24.1
MacOS 14.3