The difference is that in Bush v. Gore, the U.S. Constitution clearly gives Congress the authority to lay the ground rules for Presidential elections. When the Florida Supreme Court issued a ruling calling for a statewide recount that extended beyond the original certification date for the Electoral College, the U.S. Supreme Court had no business getting involved. The original certification date should have stood, and if Florida couldn't get its act together to meet that deadline (for whatever reason) then their electoral votes simply would not have been counted.
That appears to be more a distinction than a difference. Someone would have addressed the issue whether Congress in refusing to count the electoral votes, giving the election to Gore and thus violating Bush's 14th Amendment rights, or the USSC in deciding that standardless manual recounts constituted a 14th Amendment violation. Perhaps the USSC accepted jurisdiction following the Florida SC decision knowing that ultimately it would get the case. Let's face it...it was an equal protection issue, even if premature.