My theory has always been that Thomas Elder was married - he was the farmer in Glenbeich and I think that he had a number of other children. I have been unable to trace them properly, but there is an entry showing that Glenbeich farm was leased to Thomas and Thomas Elder in 1777, There is also a will, dated 1785 in which a Thomas Elder in Bents (West Calder, Lothian) leaves money to his son Thomas Elder in Glenbeich, I therefore assume that he was a co-signer for the lease of his son.
There's a William Elder in Glenbeich, son of Thomas the farmer, and I have therefore always assumed that he is a half brother of the illegitimate Thomas.
Whether the farmer himself was married or perhaps a widower I do not know, but somehow I don't think they lived together as a couple. She married John Thomson a farm labourer in Port of Menteith when her son was 12. I always assumed that she had worked on the Glenbeich farm when Thomas seduced her and that she was not allowed to stay when her pregnancy became apparent. At the time of the christening she is "late of Glenbeich". The info of the will from 1785 indicates that this Thomas Elder died in 1808, but it isn't clear if that is indeed when he passed away and there are no other records of his death.
Alexandrina remarried in 1791 and I have always thought that this was before the father of her child died, but maybe that wasn't the case.
Interesting, have to give that one some more thought.