I found a workaround on the forum of Starling Framework: http://forum.starling-framework.org/topic/iphone-6-question
https://forums.adobe.com/thread/1571152
I simply used IntelliJ to do the .ipa build, then after the error (but successful .ipa build), used ios-sim with the unzipped Payload/_.app using lines like the following in the command line to launch the app running in the simulator:
ios-sim launch ../../Payload/_.app --devicetypeid com.apple.CoreSimulator.SimDeviceType.iPhone-6 or ios-sim launch ../../Payload/_.app --devicetypeid com.apple.CoreSimulator.SimDeviceType.iPhone-6-Plus