Tiger, I am a Co-Mason, which as every other "masculine rite" Freemason will tell you is pretty esoteric. For one, we admit women to all rites and rituals. For another, we stem not from the United Grand Lodges of England but from the Grande Loges Symbolique of France. However, we too insist all candidates affirm they believe in a Supreme Being.
Jesus is certainly mentioned in readings from the Bible. And we do have our Orator read from Sacred texts. I read from the Book of Titus in the last Blue Lodge I attended (I was Orator for that ceremony).
I have never heard Baphomet used in any Masonic service. I think you are going back to Levi, Jack T. Chick, and Taxil. Baphomet is the name supposedly the Templars used. It is probably a corruption of Mohammed. It could also be any number of imagined connections with the word "Sophia" (Wisdom). Torturers make things up and make folks confess to them. I know, I was tortured when I was in the US Army.
We have had to find a non-sectarian name for the Supreme Being, you know, since we have Christians of all denominations, Jews (who would never pronounce the four-letter name), Muslims, Buddhists, Hindus, Taoists, etc. We leave those trappings of religion outside of the Lodge. We do not argue about the afterlife. Rather we speak about matters of how to live our lives in peace and harmony, on the Level with each other, walking upright on the Plumb, dealing with each other on the Square.
You know what else? We take those values out into the world, too. We do not just treat fellow Masons that way. We try our best to treat everyone that way. Jesus told a story about a very righteous Jew who was beaten and robbed. Everyone passed him by, but one fellow from Samaria. Samaritans were despised by the Jews. Absolutely! And yet, Jesus said that by that Samaritan's act we should all learn. Well, Freemasons are doing our best to. And when we find you beaten and robbed on the side of the road, or just stuck, or maybe your kid is sick, we do not ask what religion you are or even if you are a Freemason; we just help.
So there is my view,
A Master Mason
American Co-Masonry
Hiram Lodge (Santa Cruz, CA)
Amon Ra Lodge (Los Angeles, CA)
Sapientia Lodge of Research (Larkspur, CO)
Adamant Mark Lodge (Santa Cruz, CA)