Phaedrus, I have carried the normal sizes for quite some time to give increased water carrying capabilities to packs and bags. These have rings for a shoulder strap to allow carry by itself, which is useful at times. I recently purchased some 1.5 liter Nalgene bottles which are too long to fit in the normal size bags. I also have a Fifty/Fifty stainless steel insulated bottle which is longer than normal as well. I was hiking in Death Valley and my lexan Nalgene bottles were getting so hot that the water was almost undrinkable when they were carried in the mesh pockets on my backpack. The bottle containers help to keep the water insulated and cool. I found that my single wall stainless Nalgene bottles also stayed much cooler and drinkable even in direct sunlight.

Yee, you are correct that the velcro serves little practical purpose other than marking in some way. It can be removed easily enough.