He still faces legal challenges because Pakistan's Supreme Court may rule Musharraf is ineligible to hold office as president. The second runner-up will take office instead, as the constitution stipulates.
Musharraf is facing a great deal of opposition. They demand that Musharraf abandon his position as Pakistan's military chief before seeking another presidential term.
90% of the overall votes are cast for Musharraf but there will be few people who can see it as a credible, normal election when a large number of his political opponents have said they do not want anything to do with it.
As on many points, Pakistan's national security depends on an Islamist, Pashtun-dominated régime according to Michael Scheuer's analysis (Imperial Hubris pp. 54-56) and I believe he is correct.