Nope, not a pain at all (I thought it would be as well before buying), it lays "flush" with the tailgate cover --- the tailgates with the step handles have a factory cover the keeps everything flush when in the down position. I've loaded many motorcycles into the back and its never a concern....same thing with large boards, etc. Its definately worth it for sure, now, would I specificaly order it from the factory as option in the future....hmmm, don't know, but ours was already on the lot and had the option. One thing to note, tailgates with the step are reinforced internally (strengthened) to compensate for the weight load when the step is deployed, therefore, if you haul 4 wheelers or motorcycles with the back wheel(s) on the open tailgate, its nice to know the extra weight will not hurt it (unlike regular tailgates which have a tendancy to "bow" over years of abuse)... all food for thought, depending on your needs.
2010 XLT Screw 6.5 box XTR pkg, 5.4, bike hauler
2010 Mazda 3 Sport, Black mica, commuter duties
2008 Kawasaki ZX-6R - race ready (track duties)
2002 Honda Foreman 4X4, 26`ITPs, mud toy