You should be able to correctly code using two different ANE's, one for each platform, but it does really depend on the ANE.
Most provide a isSupported flag to allow you to determine programmatically whether the extension is supported on the current platform.
if (ExtensionA.isSupported)
{
// Use extension A
}
else if (ExtensionB.isSupported)
{
// Use extension B
}
It's also worth noting that if the extension isn't correctly implementing a "default" version (i.e. one that gets used on unsupported platforms) this may fail. Really comes down to the ANE implementation.