A possible civil birth record for your Thomas McGrath 4th July 1891, parents John McGrath and Mary Anne Farrell, residence 74 Patrick Street, Dublin City. Father occupation Carpenter and informant for the birth was an Anne Kearney.
for ref., the 1907 marriage describes John as a labourer and the grooms address as 25 Charles.., the bride's as 5 Long Lane, witnesses are Patrick Robinson & Katie Kelly - so the groom's address fit's with that 1901 census you mentioned.
I havnt found births for the two sisters to confirm the mother's name so far.. still searching for those..
p.s. marriages uaually took place in the bride's current parish - so the groom may have been born in another part of the city.