This is Brother to Demons, Brother to Gods by <PERSON>. Not everything matches your description, but enough matches to make a positive identification.
It's set in a distant future where the original humans (the premen) have used genetic engineering to produce new species of humans who have largely replaced them. These new species are the trumen, the mumen and the stargods who are so advanced they are effectively gods. (There are no pi-men or phi-men in the book.)
* Many parallel universes had been "mapped" and some were flagged as fatal to try to enter because they were "anti-matter" based.
The book opens with:
The multiverse creates itself.
It had no beginning; neither will it end.
Each new universe is wombed as a fire-egg, born through a contracting black hole. Expanding in space-time, ripening new black holes, it sows the eternal manifold with new fire-eggs of its own. Cooling, each new cosmos gives birth to galaxies and suns, to worlds of life and change, sometimes to intellect.
and we find that half these universes are anti-matter:
"One word of warning." The piercing squeak cut him off. "If you ever find your way to another universe, enter it with caution. Half the early cosmic explorers never came back, because they weren't aware of a law of symmetry that rules the multiverse. Every alternate space-time expansion produces antimatter."
* One of the characters was a dwarf-like human who chose to be ugly
The ugly dwarf is <PERSON>, who is one of the gods but who is deformed because he's the result of an experiment that went wrong.
The creature stood perched on a high sandstone bench, peering down at them with a single bright green eye. Less than half human, it looked monstrous. Its arms and shoulders were immense, the lower body dwarfed, giant hands brushing doll's feet. Naked except for particolored fur, yellow-and-black, it seemed sexless. The head was pink and bald and baby like, the left eye squinted shut, white teeth flashing through an impish grin.
...
"I'm a god—a botched god." With a startling show of power, it bounded off the floor and dropped lightly onto a tabletop before them. "A failed creation." The fat pink face grinned wryly. 322
"Though the Creators were rebuilding their own genes from generation to generation, they never fully overcame their preman limitations. Sometimes they blundered. When old <PERSON> set out to make the stargods, his first attempts went badly wrong. Most of them had to be destroyed—often in haste. I was more fortunate.
* Another character was a woman/goddess who was bored with society and went on "vacation" to explore other universes.
One of the characters is described as A lovely young goddess, touring the sacred sites of her ancestral Earth though I don't think we ever learn her name or indeed much about her.
* Some of the sub-humans had designations like "Mu-Men", "Pi-Men", and "Phi-Men." Each greek letter had different abilities and purposes. Some were used in gladitorial combat arenas for entertainment. Others were pets or bodyguards.
As noted above there are premen, mumen and trumen, but no pi-men or phi-men.
* The characters accidentally stumbled on our universe by accident. Our universe was incorrectly mapped as an anti-matter universe.
It isn't our universe that was incorrectly mapped, but a universe like ours. It was found by <PERSON> by accident:
"They'll never find us," <PERSON> whistled. "It's a place I discovered myself, but only by an accident I'm sure they won't repeat. On the way here Zhondra was giving me a lesson in transvolutionary navigation. By what should have been a fatal mischance I skipped the ship through a forbidden discontinuity, into a universe that had been charted as antimatter—"
"Oh—" <PERSON> gasped.
"But it wasn't." <PERSON> gave her his impish grin. "We didn't die. It turned out that the charts were wrong. Before we got out, Zhondra had located a Sol-type sun with at least one friendly seeming planet. 322