Charles McDonald was by all accounts a very formal and straight-laced man. His wife, Emily, was formerly married to a Henry Stratford, who died in 1892 following a stretch in Pentonville for 'bigamy and numerous other felonies'. 'Daisy' was the youngest of the Stratford daughters, and adopted the name McDonald, as did one of the other stepdaughters, Alice Henrietta Stratford. Our suspicions are possibly with Charles' younger brother 'Thomas Stuart', who lived with them on occasions. He appears to have something of a track record: a shotgun marriage in 1895, and then marries again as a 'widower' in 1909, although I can find no death record for his first wife, Sarah Jane Few. On the 1901 census, Charles' Wife Emily at Crampton Street, Penge, with Flora (legitimate daughter by Charles) and Daisy (stepdaughter), but as you observe no Charles-possibly working elsewhere on the census night, but as you infer, he can't be wholly discounted as Nella's Father?