Ok all, I think I may be on to something...I have been checking and rechecking the Aitken brothers and their possible origins based on any matches with the recurring family Christian names (Munsen/Munsden, Borthwick, Moffat etc).
I looked at the names as possible misspellings and have found an Aitken family with a matriarch called Isabella Berwick Aitken. The Berwick name continues through that family (see Isabella Berwick Aitken Hamilton). Importantly, Isabella and husband William Aitkin had a son John who married Catherine Lumsden, sometimes recorded as Katherine Lumsdale. Isabella and William also had a son James (b. 1795) which puts him at the right age to be a parent of Thomas and George Aitkin/Aitken.
The family is Fife based, but some members appear to have joined the drift to Midlothian. I haven't yet traced what happened to all of them, but so far I have:
William Aitkin and Isabella Berwick m. 5 Nov 1785, Kennoway Fife.
Children (all born in Fife) are:
Jean b. 1786, Kennoway (m. John Thomson)
John b. 1789, Markinch (m. Catherine Lumsden, 1811, Largo)
William, b. 1793, Kennoway
James (Aiken) b. 1795, Kettle
David, b. 1800 Scoonie
Agnes, b. 1803, Scoonie (m. William Young)
Alexander, b. 1806, Kirkcaldy (m Janet Paton)
Alexander Aitken and Janet Paton had a daughter called Isabella Berwick Aitken (later Hamilton).
John Aitken and Catherine Lumsden had a daughter called Agnes Berwick Aitkin.
I haven't yet traced what happened to William, James and David Aitken, but James looks highly prospective. If he and his wife died young, then it could explain the confusion in various records (James/Isabella or John/Margaret) and the importance of the names Berwick/Borthwick and Munsden/Lumsden.