1) I have used Magellan handheld GPS inside my TCH , I had no problem with reception whatsoever, even if I had it sitting down inside cup holders in the center console. I don't think hybrid system has anything to do with GPS. Probably combination of poor antenna and windshield, but as I said I had no problem. Never used 680, can't say if there is anything specific about that particular GPS, it should work as usual.
2) I like my build in navigation system, just for the screen size alone. I think you get better radio, better display for phone book, much more comprehensive display of hybrid system and fuel economy, you can input scheduled maintenance work, nothing you can't live without, but it's nice. I can't say it's worth $1200 extra for you, if I was doing it all over again I would get it again, YDMV.
3) I have no experience with your phone, it works great with my LG8300.
4) It's impractical for driver comfort, (did you get heated seats?), warm up past first 30 seconds is waste, it would probably take longer also, since driving will force ICE into higher RPM
5) Yes, you can reprogram doors opening sequence yourself, can't think of any must have changes. There is a way to activate alarm system siren, using build in security system in case of break in, but you need dealer's programming tool and non official procedure, not sure if dealer would be aware and willing to do that. Otherwise I think the car is pretty good with factory settings.