There is such a strong sense of familiarity, trust and respect Mary has for Thomas. I'm specifically speaking about the scenes where she so casually, takes her hair down in front of him like he is a life long friend. Where she hugs him and breaks down, and she quite literally has to be pulled off of him. And then, when she is telling everyone how much he's helped her, and gave her her new horse.
I think it's such a contrast to what Thomas is used to working with royals, especially when it comes to royal women and hair.
I'll never forget the scene in the book, when Anne invited Thomas into her room in the middle of the night, and her hair was out, and she was simply in her night gown. That was a power play by Anne, which Thomas realized. It was showing him that to her, he was less than a person. There was no need to be modest around him because she didn't register him as anyone of note - he is even compared to her fool in that moment. Looking for the page/quote where Thomas explains it...anyway. But why cover your hair for a man you don't consider a man of note?
With Mary it's different. The lack of gable hood, the familiarity, the ability to be around her at her most vulnerable moments. In contrast to Anne, who saw him as nothing, Mary sees him as everything in these small moments. Which is why I think he was so taken aback when she embraced him. Because he isn't used to that. There is no ulterior motive. The last time he was around a royal woman with her hair down, and she was undone, it was the emphasize how little regard she had for him.
Now, when a princess does it, it's to emphasize the opposite. That she sees him as a person and she is so grateful to him.
One of the things about Wreckage is that I've been trying to pay attention to what Mark Rylance is doing when other people are talking and one of the main things he does is to look away breaking eyecontact with the speaker. When Henry is speaking it's like Thomas can barely look him in the eye esp. in the first few scenes and it isn't until he makes the comment "I sometimes wonder where you came from?" and Thomas says "Putney, Majesty" that things seem more normal between them.
In the scene with Mary, he averts his eyes because she has her cap down and then added to that the awkwardness of the hug he really can't pull away though he looks like he wants to.
In the scene with Jane though he does not break eye contact with her, he looks at her the whole time through the whole fur stroking interaction...
My own take on all of these is that they are all trying to manipulate him through their own use of their person. Henry uses his powerful size to intimidate. Crom doesn't frighten easily but there are numerous times in Season One where it's clear he's physically afraid of Henry and I'm sure those incidences are going to ramp up as Henry deteriorates.
Jane is clearly flirting in her own extremely subtle way, breaking protocol, and getting away with it out of sheer guilelessness. Her double entendre, "Do you want to kiss my ring or anything" could not have happened in Anne's court because no one would have thought Anne would have made such a verbal blunder.
Mary may be trying in her own awkward way to force an intimacy with him with the cap. Then in the next scene saying:I am bound to you...I will pray for you. If you look at it in the rules of chivalry he might have been expected to be engaged to her after seeing her hair down. Had such a thing been widely known it would have been a scandal. I think there's a moment of panic in Mark's eyes in the chapel scene when she says "I am bound to you" thinking perhaps of hand fasting, which was the common law way that many people were married outside the church. The ceremony was literally binding a rope or tie over both parties hands. But Mary seems so innocent that I think Crom just has the wrong end of the stick maybe...