The reason you are seeing the left / right flip is because one diagram is showing you the "die" relationships while the other is showing you the Package relationship.
The "die" is left / right flipped as it is mounted upside down in the package - thus the name flip chip packaging.
This is a 'common' problem many before you have faced, and it is a good thing hat you are checking all this out NOW before you lay out your board.
So both are "correct".
I do not think that in the I3 speed grade you will be able to get 533 performance.
DDR2 or DDR3 @ 400 is a good question to ask about.
If you are designing for the future - then DDR3 will become cheaper as time moves on.
If you are making a board now for small run sizes, I think that DDR2 is still cheaper.
Additionally - I believe once you dig in you will find that for DDR3, you will need to "burst" in more rows of data then in DDR2 and if you are jumping about in your data set, this could take longer for the controller in the long run, whereas if you are moving large amounts of sequential data, this might be better for you.
It all depends.
You have lots of reading to do on both memory type and some system data flow analysis before you can make that decision.
With 10.0 - I still think that you will be limited by the I3 speed grade limit - not by the newer tool.
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