I leave the plates on all the time. As for the safety stop screws, it's always been my habit to set down the camera with the left side (and lens) resting on the surface, not the bottom, so no issues with lens plate or body plate (if any) screws. The lens plates do not present any problem or require collar rotation in the bags I use (e.g. Lowepro Toploader 75 AW for the 100-400L). The 1D X L-bracket makes it a little more challenging to zip a Toploader closed, but it works (and that plate is RRS' new modular design which is awesome - the side of the L-bracket can be removed if desired leaving just the bottom plate, and the allen key to do so actually stores right in the plate!).