But even with a 99-pound limit, it might still be advisable to pack your gear separately. That's because the TSA will almost certainly open your bike box to inspect it (since it doesn't fit in the scanner). When I pack only the bike and nothing else in the box, the TSA can inspect it without pulling the bike out of the box. They just open the top and look in.
Good point. At my local airport (BWI) they seem to open the bike box every time. When I have flown home from other cities they more often have not. The TSA has been pretty brutal in their handling of my stuff. They opened the little tool bag under my saddle, dumped the loose contents in the bottom of the box and ripped the stiff plastic lining out of the bag. On the same trip they broke off one of the cable adjusters in the braze on.
Funny thing is that the only times in recent memory that they didn't open the bike at BWI were the times that I had all of my gear packed with the bike. Both times it was in a soft case rather than a box. Not sure why they didn't open it these times. Maybe my soft case fits in the xray machine? If so there may be an advantage to taking off both wheels and packing in a smaller box, bag, or case.