I have gone for the low chassis version for both my previous 1200 and my current 1250, and can definitely recommend it. The low chassis will not work any less well regarding maximum load and suspension sag as the spring is sightly harder to compensate for the slightly shorter travel, and both versions will therefore bottom out equally low. Although I am quite tall, I have a long torso and only average length legs, so I find the low chassis version lets me have a better padded normal seat in the high position while still being able to flat foot, which is a boon in tricky situations, especially when loaded with a pillion and luggage.
Low profile seats are all very well, but are less comfortable and cramp your legs more by increasing knee bend, especially when mounted in the low position. I road tested a standard chassis bike and don't think the low chassis bikes looks different or handles differently, and in fact the slightly lower centre of gravity is probably an advantage, while any reduction in ground clearance would be minimal. This would probably only be a factor in extremis during track day type riding.
Just sitting on the bike and getting the normal 30% or so of sag reduces the height difference between the two versions, as the longer travel suspension compresses more for a given load, and bear in mind that both versions get progressively closer to equal ground clearance as the suspension further compresses due to road surface or cornering loads, until eventually they bottom out at the same level.