I see some smaller carrying cases are designed only for when the props are removed.  Looks like some larger cases allow leaving the props on.  I would suspect with the foam pushing down on the props that they might warp if in a hot car?  



If you did leave them on, can you rotate one or two to make it fit in a case without rotating the others?  Or are they in sinc so spin one = spin all?

They are independent motors, so you can rotate them to fit, each one pointing in a different direction if you like. I never thought about the warping bit though.

I keep mine in the case with props on (http://microraptorcases.com/prod ... o-fit-the-phantom-3) and it has two posts to keep the blades from moving while in transit.  The blades don't rest on the foam nor does the top of the backpack apply pressure as it is protected by the posts and the shell of the Phantom.  I have had no problems even when driving through the desert between San Diego, LA and San Francisco.  I do use the carbon alloy props sold by DJI, however, if that may make a difference.
edit: I stop and fly when I drive; not that it sits in an air conditioned car the whole way...

Cases by Source's cases don't require you to take off your props.  The RecoCell Foam they use adapts to the shape of the blades and cradles them, without warping them at all.  Check them out:

http://www.casesbysource.com/brand/casepro-drone-quadcopter-cases