This skyway has been like this since beta. KI said it has already taken steps to shorten the leash on them (distance the bone drakes can move). This makes it a bit easier for people to make it into that skyway without getting caught. Slower computers tend to have more trouble with this area. I try to stop my ship as soon as I enter that skyway, or turn to the right and see where I end up before moving forward (sometimes it helps, sometimes not).
I have had no problem with the Bone Drakes of Dragonspyre (Avernum) as long as I stay in the Windlanes. I don't know if it makes a difference but I have been using Pirate type ships for transiting Dragonspyre (Avernum).
Avernus has been that was since beta. Be thankful that now it drops you off heading towards the windlane and not in a pack of bone drakes like it did in early beta. As long as you stick to the windlane and try to avoid flying directly into a pack of bone drakes you should be fine.