Yes, this is fine. During the auto-focus, what is happening here is the bed is moving away from the tip where the beam exits the lens tube for thicker stuff and closer for thinner things, but the top of your material will end up at the same location in space and should always be a certain distance from this tip.
Think of it this way, the properly focused height is the top of your material. You are moving the bed to give room for the rest of the object to fit inside your laser. The top is always the top and should be the same distance from the tip. You are only moving the base support (the bed) for your material so that the top stays at the properly focused height.
