If you get a kombi you will end up with the windows, tailgate, higher step etc, and seats which you can sell on and hopefully make back up some of the difference in price initially. At least, this is what we were recommended when buying by the company who will be converting ours.
Personally, I wouldn't bother with Factory Nav, as it's not as good as google maps with App connect (I have it, and use google maps!). I wish ours had a comfort dash and adaptive cruise, but we bought a showroom model, and therefore didn't have the option. Also, 2+1 rear seats are more desirable if you do get a kombi.
Edit, oh and LED Lights! They are awesome. Apparently the standard lights aren't....