Thanks - we do have a crate (but it doesn't fit in the Octavia), removing the luggage cover isn't an issue, I'm not fussed if we have to take that out. Our dog is a Labrador, I'm not sure how comfortable she'd be in the crate listed but I've seen some car specific crates that might be suitable. I'm trying to work out a compromise between making sure there's enough space for the dog and retaining some luggage space in the boot.
I thought the variable floor was on runners and could be slotted into one of two positions, maybe I've not understood it properly. So from your description it sounds like the fixed floor in my car would be the same height as the 'variable' floor removed/lower position?