Hi Skoosh,
Yes, Google....where would we be without it! I keep picking up snippets of information, but didn't have all that you mention. I knew Thomas was a bit of a lad and had several mistresses, however, there appear to be 2 of Thomas Lyon...father and son.
The first was born around 1548/50 at Auldbar, to John Lyon,Earl of Glamis and Janet Keith. I couldn't see him being the father, although he had several wives. But he had a son Thomas in about 1570. I considered him to be the father of Alexander, as he is the one that was 'Master of Glammis', while being heir presumptive. ( I got this from Ancestry and Google). He relinquished the title twice, but was actually Master when Alexander was born.
I have found him as being married to Agnes Gray, but the elder Thomas was also married to her....or the records have become confused.

I have looked on The Peerage site as well for information on them. So far though, Alexander's mum is just plain 'Mrs Thomas Lyon'.
I must keep digging, he must have been honoured to have so many nobles around him when he was born/baptized!
I hope that 400 yr old clerk is having bad dreams about his handwriting

. He must have been very old or trying to develop his own secretary hand.
Sheilah