These are great questions.
I have a question about the transition from 2nd stage to 3rd stage individuated. From what I understand about these stages, a soul moving from 2nd stage to 3rd stage is moving from being alienated from the society in which they live and defining themselves as utterly different from others to attempting to reintegrate into society, bringing their uniqueness as what they have to offer to society.
For starters, I would not put it that they were trying to reintegrate into society. A Soul that has reached that point is never going to be able to reintegrate into society. I would say they are going to want to carry out their unique life purpose, on their own terms. For some Souls that will require playing a role that will put them operating within the mainstream. But they are not really reintegrating, because they are going to play that role out on their own terms. They will operate WITHIN society, but not as part of it. They are always maintaining allegiance to their unique inner vision.
In this stage of evolution could someone still have the fundamental mistrust of the 2nd stage, relying only on themselves, and yet be attempting to integrate their talents through their work into the mainstream in a unique fashion?
In most cases, that is EXACTLY what would be happening. Even in full 3rd stage they are still going to rely only on themselves. At the beginning of 3rd stage, that fundamental mistrust from 2nd is still going to be a strong archetype. That mistrust NEVER goes away. As they advance into 3rd stage, they simply become more accepting of its inevitability. It just becomes part of what is, something they have to accept to fulfill what they are here to do. Even though they are thoroughly alienated from the mainstream, they accept they have to operate within it anyway. Whereas second stage is less accepting of that.
Also might there be a tendency to live a "double life" because of the insecurity about honestly presenting themselves in society or is this more of a 1st stage individuated trait? For example, might someone transitioning to third stage be married and have children while living a double life in the BDSM community because their fundamental distrust of society has not been completely resolved? Or is participation in subcultures part of what defines the individuated stages as a whole?
Again, once someone is in individuated and beyond, the fundamental distrust of society is NEVER resolved. It is just accepted as a given.
As far as your example, the motivations for that behavior would be different in 1st and 3rd stage individuated. 1st stage would be more about hiding it away out of fear of showing up as who they really are. There are various reasons that might appear in 3d stage individuated. The person could have realized the BDSM expression is a valid part of their evolutionary needs in the present life. Their role in society, to fulfill the mission they have as a 3rd stage individuated person, might require them to live in such a way that openly revealing behaviors like that would cause them to get fired. Thus they could not fulfill their mission. Yet to truly be who they really are they have to engage in those activities. So they might realize they can't reveal their true nature to the world at large, thus create what appears to be a double life. I'd suspect that in most cases the spouse would be aware of this dual life - the person would have clued the spouse into their actual nature, and the spouse would have come to accept that this is necessary. Of course some people couldn't handle that, and it might in some cases lead to the termination of that marriage. But if the spouse could understand, they would accept the circumstances - that would be part of the spouse's evolution.
Thus the person would be concealing their activity not because they were ashamed of it but because that was necessary for them to fulfill their mission. They would own who they were, those parts of themselves, and how they needed to construct their life in order to get all the necessary parts working relatively harmoniously.
There are no doubt many other possible scenarios why such behavior might exist in 3rd stage indiv. I just detailed one possible set of circumstances. Each Soul will have its own unique reasons and background. In all cases the inner motivations would be quite different between 1st and 3rd stage indiv.
Hope this is helpful