are there any differences between referencing signal to VCC or GND planes?
As long as GND and VCC are connected by several capacitors at both sending and receiving end of signal lines (as they should be, will be in high speed design), AND where the return current changes planes (which you should try to avoid) then it doesn't matter which plane the return current flows in. The return current is only interested in the AC impedance of the path. 

Note that signals carried in layers 3 and 4 will be referenced to both return planes. You have the opportunity to choose core and pre-preg thicknesses so that the same widths on all layers could give you the same impedance, but if not, use different widths on 3 and 4 (which are offset stripline) to 1 and 6 (which are microstrip).