Your third choice must be from a different block from your first or second choice.

The way I took it was that your first two choices can be from the same prefecture if you wanted, but your third one had to be from a different prefecture. Basically I looked at it as, I was able to request my first and second choice from block C, but my third had to be elsewhere. I think the point was to keep you from requesting all one prefecture. I'm not sure that the order matters though, as long as you don't have all three choices being from the same block.

If you're really that worried and you're flexible, you could possibly just do it this way: F, F, E and only put a reason for your choice in the E section since it was actually your number one. This way they may give consideration to that one because it has a reason. Remember, you may not get any of these placements, so I wouldn't get too caught up on why you need E to be number one unless it's super important. Like for me, I want to be near Kanazawa since it's my city's sister city and I mentioned it in my SOP. My other choices are still close enough though, so it flows nicely.