I wouldn’t bet the farm on that. Read Letters from Earth.
There’s a difference between satire of the faithful and a denial of faith. Twain’s description of the fly as God’s most beloved creature in Letters from Earth is wonderful satire, as is his mockery of faith healing in Christian Science, or his sneering descriptions of “the pilgrims” in the Innocents Abroad. I also don’t think Twain believed in time travel because he wrote a Connecticut Yankee in King Arthur’s court.
It wouldn’t bother me one wit to find out that a recently uncovered will of Mark Twain includes the phrase “I deny the existence of God.”, since I don’t draw upon him as a testament to my own faith. Stating he was an atheist by cherrypicking his works doesn’t work for me though since he didn’t live the life of an avowed atheist. Setting his self identification as a Presbyterian aside, Twain was a Freemason (belief in a higher authority is a prerequisite to membership), he also spent many years researching and writing a respectful biography of Joan of Arc, whom by all accounts he deeply admired due to - not despite - her faith.