Reverse timeline. Births, marriage and deaths are from the index at Scotland's People.
1911 Census index: William Cloonan, 40 and Elizabeth Cloonan, 35, in Edinburgh Canongate.
1909: Alexander Bowden McLaren marries Margaret Meikle McIntyre in Edinburgh St Giles.
1901: William Matthew Cloonan, 3, dies in Edinburgh Canongate.
1901 Census transcription: William Cloonan, 30, railway porter, born Ireland; Elizabeth Cloonan, 35, born Canongate; William Cloonan, 2, born Newington; Mary A Cloonan, 24, born Canongate, at 14 Canongate, Edinburgh.
1899: William Matthew Cloonan marries Elizabeth McLaren in Edinburgh Canongate; William Matthew Cloonan born in Edinburgh Newington.
1891 Census transcription: Alexander Bowden, baker, aged 72; grandchildren Elizabeth McLaren, 16; Margaret McLaren, 11; Alexander McLaren, 9; William McLaren, 6; all born in Edinburgh, living at Calton Hill, South Leith.
1887: Elizabeth Bowden or MacLaren dies in Edinburgh St Andrew aged 43.
1884: William McLaren born in South Leith.
1881: Alexander Bowden McLaren born in Edinburgh St Andrew.
1879: Margaret Bowden McLaren born in Edinburgh St Andrew.
1875: Elizabeth McLaren born in Edinburgh Canongate.
1874: William McLaren and Elizabeth Bowden married in Edinburgh Canongate.
1871 Census transcription: Alexander Bowden, baker, 52; Elizabeth Bowden, wife, 52; Elizabeth Bowden, daughter, 24; Margaret Boyd Bowden, daughter, 20, at Fleshmarket Close, Edinburgh St Giles.
27 August 1870: William Mathew Cloonan, son of William Cloonan and Helen Docherty, born at Macroom, County Cork, Ireland.
1861 Census: Alexander Bowden, 42, born South Leith; Elizabeth Christina Bowden, wife, 42, born South Leith; Elizabeth Bowden, daughter, 15; Margaret Bowden, daughter, 11; William Alexander Bowden, son, 8; at High School Yards, Edinburgh Canongate.
See what you make of this. Without looking at the original certificates I don't guarantee that every listing is relevant, but it does all hang together and suggests that either Alexander or William McLaren must have been the father of Ian and Patrick McLaren.