Operating system: Windows-10-10.0.19041-SP0 64 Bits
Graphics card: GeForce GTX 1070/PCIe/SSE2 NVIDIA Corporation 4.5.0 NVIDIA 462.59
Broken: version: 3.0.0 Alpha, branch: master, commit date: 2021-05-21 13:09, hash: rB5158d1b42dcd
Short description of error
Mantaflow doesn't notice when geometry nodes are used to modify a mesh. Looks like it could be related to if the object is keyframed or not.
Exact steps for others to reproduce the error
Open the attached file and in the Fluid Domain click Bake All.
Run the animation.
The inflow follows Cube1 but not Cube2. The difference between the cubes is that Cube1 has a keyframe on location, but it seems like it doesn't matter which property is keyframed.