I would get in touch with them and amend the booking. Personally, a roof carrier is preferable, boot carriers are an issue for three reasons IMO;
1 - You can't access your boot / hatch contents
2 - If you have 3 or more bikes on the back, you are likely to be obscuring the lights and or number plates - so you'll need a lighting board (
Halfords)
3 - I find rear mounted racks a lot more unstable.
Of course the downsides of a roof mounted rack are:
1 - A pain to get the bikes up!
2 - Fear of height restrictions!!!!!! - I destroyed a roof system and bike once (how stupid am I).
PS, I've used both types of carriers regularly.
Enjoy!