Thomas's DC in 1863 is hard to read isn't it! More importantly, I wonder if son-in-law Michael may have misreported details regarding the surname of both Thomas's wife Jane and his mother's surname (not uncommon). Both as you say look the same.
Thomas's details on IGI (marriage and children's births) clearly show Jane as MacDonald. Have you looked at some of the children's DCs, what do they show for mother's maiden name? From the census info for Thomas, it looks like Jane wife had died by the 1841 census. If she had been dead for some time, it may explain the vagueness about her surname.
You have an actual extract for Thomas's birth with father as Thomas and mother as Alexandrina. I agree the birth could have been illegitimate and would explain Alexandrina's marriage some 10 or so years later (or she could have been widowed early and remarrying).
I wish I could see something more definitive for you but as it is, I think I am just treading the same steps as you....
Which is you line, is it Peter? How has he been transcribed on his DC index is hard to say, he certainly not jumping out
Thomas son had an inventory following his death in 1889:
Elder Thomas 07/10/1889 merchant in Kilsyth, d. 15/07/1889 at Kilsyth, testate, spouse is Helen Mason or Elder Inventory; Extract Registered Trust Disposition and Settlement; Codicils Stirling Sheriff Court SC67/36/90
I'll keep an eye out and see if anything new jumps out
I assume you have the early census info for them, if not let me know.