I luckily managed to get through my A Levels without any clashes like this, but a friend of mine had the issue, and was made to sit them straight after each other. I guess it's up to the school what they do, but you could always question their decision if you want (although be prepared for them not to change their mind). They will be thinking about purely what's easier for them to do, but just point out your reasons for preferring another option. Obviously if there are a lot of people who have the issue, your choices may be limited.
On a bit of a side note, I had a friend at uni who somehow managed to end up having to sit 3 x 3 hour exams in one day, which I imagine was a bit of a ball ache. They weren't clashes though, just so happened to have an exam in every session that day.