OK. My turn.
1016 addresses travel distance (for those of you on the west coast, bear with me). Section 1016 is used when there is an open stair that can be treated as a part of the exit system. If you look at exceptions #3 and #4 in 1016.1, those are the same exceptions that used to be in 1020 of the 2006 code. These two exceptions were brought in as UBC conditions and called "exits" but as we know, by definition and exit is separated from the rest of the building. So if the open stairs can be used for egress and you measure travel distance down the stairs to the door below, it isn't really an "exit" is it? It's exit access. The fact that the UBC used the term "exit" for everything until the 1997 UBC messed with minds and kept us from getting on the same page.
So, if you have a stair that can be used in one of the exceptions in 1016.1, it means it is an exit access element and not an exit stair. Therefore the 48 inch clear width isn't really applicable since the reason for the 48 inch clear width is to allow a double carry for wheelchairs. If it's not an exit, it doesn't need the additional width since the occupants who would use them would likely be in another part of the floor; near the enclosed exits stairs. All this is predicated on the concept of areas of refuge.
The IBC was trying to be somewhat consistent in the way it was dealing with the issue. If you read the 2006 code, it referred to Section 1020.1, the prior location of those two exceptions. All that happened was that staff, obediently translated the reference. The code change that moved the exceptions didn't consider this aspect.
It might be worth noting that the Life Safety Code only allows the 48 inch reduction if there are personal assist decent devices at every floor. At least this is more consistent. It recognizes that if the wheelchair needs to get carried down, it needs to get carried down, regardless of what the stair is - exit or exit access. And now that we get only one chance at fixing these things, it will be at least 2015 before we have a code that makes sense.