There's absolutely no documentary evidence to that effect.
There was a St Domingo cricket team that most definitely did come from that chapel. It's a massive stretch to state that Everton came out of it.
Most definitely former congregants of St Domingo formed part of Everton FC when it was founded as a district team in 1879 - Cuff states as much and Keates' early history states it too - but along with other players from other churches in the area....in fact you could easily dump the term 'church' right out of the equation. The lads who formed Everton may have been formally or informally connected to churches when they were growing up but they assembled on Stanley Park as players who hailed from Everton (the district) and represented only that district rather than some notion of a religious root they'd come from.