Its less a case of comparing an auto gearbox car fitted with an auto diff, to a manual gearbox car fitted with a manual diff, as fitting a diff meant for a different gearbox would have a different final drive (think thats the correct term?).
Best way to think of it is in terms of numbers, rather than gears. If you wanted to add two numbers together to equal 10, you could use many combinations.
If we say that an auto car is 4+6, and a manual car is 5+5 (the first number being the gearbox the second being the diff).
Swapping the diffs would give you an auto car with a manual diff and a manual car with an auto diff.
Auto car 4+5= 9
Manual 5+6= 11
Fitting an auto diff to a manual car will essentially give you different acceleration and top speed; however it was my understanding (from other cars) that fitting an auto diff to a manual car improved acceleration due to the nature of the autobox. So using that frame of thought, perhaps it would numb the acceleration and in actual fact give you a higher top speed. However, whether that figure above refers to top speed or a rating of acceleration, who knows! I've only had the car for 3 weeks!
All that said, if it was me I would be looking into getting an aftermarket LSD with the ratio to suit, one that locks up better for my requirements. Whatever they may be!