Yes, there would be a contradiction. To think that there could be no contradiction stems from a gross misunderstanding of the term "votes".
Bush received more votes than Gore in Florida - PERIOD. Such was the finding of that state's Secretary of State on the deadline (both the legal one, and the non-legal one set by that state's Supreme Court). This is why Bush received Florida's electoral votes, which helped him win the Electoral College, which made him the President.
By any legal definition, therefore, Bush received more votes in Florida, therefore he is the President. Had he not received more votes in Florida, he wouldn't be President.
Counting these ballots, by whatever method, doesn't alter this tautology, since: (1) these ballots are NOT LEGAL VOTES, and (also, because): (2) the DEADLINE has passed.
The strongest statement you can make, I suppose, is that there would be no contradiction in saying that Bush is President even though the media have repeatedly attempted to cast doubt on the legitimacy of his election, by counting ILLEGAL VOTES and so on. But this is not exactly the most earth-shattering observation in the world, so I won't insult your intelligence by pointing it out. Best,