I cannot recall if I made a headcanon post about this or just went on about it with @intolerablexsacrifice but the long and short of it is, Thomas utilizes a form of classical conditioning with people who are in his sphere that he sees are in need of particular cues to respond to. The two most common cues he uses are a click of his tongue ( indicating disapproval ) or a low hum ( to indicate approval ) 

While these tricks are not something that Miranda responds to ( she saw through his game early ) the both of them utilize these against one another in a more playful manner. There is nothing subconscious about their reactions – Thomas knows when Miranda is giving him a straight up dressing down in public with a simple click of her tongue, just as Miranda knows when she has gone too far or is being teased by her idiot, constantly social experimenting husband. 

They don’t bother with humming so much – as they are married, they much prefer to use physical touch as a method of reward because it is something they both crave and are more than permitted to exchange socially. 

The difference between Thomas and Miranda clicking at one another, and Thomas clicking at James, or Peter Ashe, or even his own father, because yes he is daring enough to try that shit on Alfred Hamilton, is that with anyone other than Miranda, Thomas is training these people. It becomes subconscious to them, and it is notable especially with James and Peter, because they are receptive to it. 

Though they may not register it for what it is, Thomas is conditioning them to seek his favor – to prefer a hum over a click, to seek to avoid the sound of disappointment. Depending on the verse with James, this can be something that shifts into the same realm it held with Miranda – a means of communicating without words, without letting the world see what is really happening – a way of teasing and playing. 

Alternatively, it can remain a method of control, which shifts the power balance and keeps things from being wholly healthy between them – alternatively, it may be used as a means to communicate when PTSD is ravaging one or the other, in which case it is used as a means of helping one another navigate troubled waters and is more of a healing tool than a manipulative one.