Yep, just tried the Mac version and it allowed me to do this. Start the first download as usual. Then go to the BirdsEye menu and choose download. The dialog box will appear again and you can select another area while the first is downloading. After selecting it will show a "0%" label while the first image continues to download. When the first image reaches 100%, the second download will start.
I only tried this with two small test areas, but I'm sure you can use the same technique for more and larger areas.
I only tried this with two small test areas, but I'm sure you can use the same technique for more and larger areas.