Can shimano di2 be programmed to be automatically readjust shifting for different hub/wheel types?
Quick answer: 

You would need to use a PC, and you would need to make sure that the wheels had reasonably close original chain line positions for this to be possible. If not, then no, you can't do this.

Long answer:

Shimano's E-Tube software does allow you to save presets for adjustment and switch settings.  That means you could have multiple presets saved for the electronic portion of the shifting adjustment.  

However, if the difference in required settings between the wheels is more than could be adjusted for by adjusting cable tension on a mechanical system, then you will still need to adjust the limit screws on the rear derailleur.  

Since those are still a manual adjustment, there is no way to ensure that swapping between wheels on an electronic system is possible using only the preset system.

Also, there is no way at present to swap between presets on the fly with the road Di2 system, so you would need to plug the system into the E-Tube software on your PC.  

There is the the possibility that this might change, since the new 2015 XTR Di2 system has the ability switch between shift maps using the SC-M9050 Display Unit. At present, though, shift maps only affect the order of shifting for XTR's Synchro shift system.  They do not allow shifting between preset shifting adjustments.

Since the Display Unit is functional with the road Di2 systems, it is possible that a firmware update could enable the ability to swap between presets.  Without the ability to make the manual adjustments the preset swapping would have limited utility for this purpose.