Why is the second sentence more natural in common usage? Because no one, no where can fortell the future with total accuracy. Perhpas Gap will close only 650 of thier stores, leaving them with 32% (don't do the math) by the end of 2013.
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ryotaro1) They will close 34 percent of Gap stores worldwideYou left out the by-phrase, which is the most important part of why they used will have.
2) They will have closed 34 percent of Gap stores worldwide