the signal loss from the trunk shouldn't be too much of a problem altough usb stuff can sometimes act up over 10', there are usb extenders though that boost that limit. the touchscreen wakey thing sounds good but you have to test it, not to sure how reliable that may be if it even works at all.
one advantage you'd have with the dock is you can hack into the power switch on it if it has one & have a hardware startup solution over a software one, which should be much more reliable & trouble free
also, I second
about dc/dc power supply, much cleaner power & more efficient.