They were hard living hard working fishermen and it would not be unusual for alcohol to encourage extra liaisons during periods ashore. William married Eleanor Bridson on 12th April 1841. She was christened on 30th August 1818 and was still alive in 1881 (Census shows Elinor Killip Widow aged 64 living with her sister Elizabeth Bell also aged 64 at No 102 Malew St). Her parents were William Bridson and Ellinor Radcliffe (interesting name?) who had children William 1812, Robert 1822 and Ann 1831 with Elinor and Elizabeth christened on the same day 30th August 1818 - were they twins who stayed close throughout their lives?).
It is interesting that Thomas and Radcliffe only have Elleanor as mother not Eleanor Bridson - but Radcliff's name might reflect his Grandmother's name which would indicate Bridson as the mother. On the other hand..
There only appears to be one William Killip in Castletown around this time who was from the Malew area and it is thus a strong possibility that he fathered all these children, but not evidence as there were many other William Killips elsewhere. Certainly a William Killip is shown as the father of two of Elinor Faragher's children - William and Andrew (I am sure William K (b1816)'s father was Andrew - thus these would reflect names of father and grandfather giving weight back to William 1816 as the father).
I think these children are of the same father, but perhaps of two mothers, suggesting that Thomas and Boyer were sons of Elleanor Bridson. I am not convinced by the wind direction! I tried to find a previous marriage of Elleanor Bridson with a Faragher but failed - although marriages are less easy to trace than christenings - and we know Elleanor Bridson Killip outlived William ....
All conjecture! Perhaps Jane Quine is the key - have you managed to find the full link with her niece Eleanor from the 1841 census or elsewhere?