My recent experience (4 flights during the past 3 weeks, just returned home yesterday): Lens stayed on camera, but extra lens (I only carried one and it's bubble wrapped) must be put in bin as well. Agents in the US and Europe handled my equipment with utmost gentleness, with both hands and one item at a time. Not one person looked through the viewfinder. The reason they touched my camera and extra lens was to rearrange them in the bin the correct way (I had BR strap on camera.)
My filters stayed inside the bag, and no one asked me to peal the bubble wrap off the extra lens.