Can GBTimelapse control the MX2 in two axis mode?
It depends on how GBTimelapse is connected to the MX2.
Method 1: NO - GBT connnects via USB to the MX2 USB connector. The issue as to why you can't run a telescope head and GBT control at the same time, is because there is only one MX2 serial interface (it is connected both to the USB port and the Ext 0 port) on the arduino.
In addition the telescope heads are only half-duplex (one wire for TX and RX), and there are a couple of resistors in the adapter to keep the TX and RX pins from pulling each other around - this results in an echo of anything sent down the serial line. It also means that both TX and RX are pulled to a HIGH state when the telescope head is connected and idle - effectively squashing any possible communication via the USB port.
Method 2: YES - Mike Lanfor put together a great 3-axis motion control tutorial on using GBTimelapse AutoRamp with a Dynamic Perception Stage Zero Dolly and Merlin Pan/Tilt head. Check it out at this link...