This looks like an instance of adjusting the data to avoid ruffling any conservative ideological feathers. I presume the speech writer(s), rather than Bush, decided to remove Jefferson's offending words.
What Bush said:
Thomas Jefferson understood that these rights do not belong to Americans alone. They belong to all mankind. And he looked to the day when all people could secure them. On the 50th anniversary of America's independence, Thomas Jefferson passed away. But before leaving this world, he explained that the principles of the Declaration of Independence were universal. In one of the final letters of his life, he wrote, "May it be to the world, what I believe it will be -- to some parts sooner, to others later, but finally to all -- the Signal of arousing men to burst the chains, and to assume the blessings and security of self-government."
What Jefferson said (The part excised from the Bush speech is italicized):
May it be to the world, what I believe it will be, (to some parts sooner, to others later, but finally to all,) the signal of arousing men to burst the chains under which monkish ignorance and superstition had persuaded them to bind themselves, and to assume the blessings and security of self-government.
Good thing Obama hasn't mentioned "monkish ignorance and superstition." It would become a 24/7 tape loop on Fox News -- proof of his deep-seated contempt for core American values.
HT: Ed Brayton