I've seen it both ways.
But that was for presention purposes (ie: crossovers inthe trunk for show off effect).
Everyone I know who has the crossovers in the trunk swear there's no difference. But, they just may not know what they're "hearing".
My passives are on short runs, but I have thought of putting them in the trunk next to my amps because I've worried about water in the doors and space issues everywhere else (well, show off the MBQuart names too!).
Sorry if that's not too much elp, maybe durwood can chime in here?