I am using Godot and I am using apply_impulse ( I used apply_force too but I didn't like the results).
The problem with physics engines in general is that they move the objects in the physics step and then apply forces to separate the overlapping objects (collision reaction). This way if an object is moving too fast there is a possibility to pass through an object or stuck inside. The solution to this is to make more steps for the fast moving objects. Godot have this but the physics engine is locked with the frame rate, this means that if you loose a frame the crucial moment then you may have a problem like this.
This is how I remember things worked for Bullet at least, cause I have read some of the presentations and techniques back in the days of the first versions. I also remember similar things about the first presentations of Box2D. Godot's physics engines are like striped down versions of Bullet for 3D and Box2D for 2D.
I Unity I do not know what they used, but I remember that they had good reaction for fast moving objects.