This is largely true. The scenario that this is largely NRE working its way through is, I believe, still the most likely case. That Bill and she have earth-shattering sex is in and of itself wonderful. What I have not liked, as you have related the story of what has happened, comes down to three pieces:Really Bill is not the problem here. Your relationship to Sam is.
1. I did not like the comment when you expressed your discomfort about Bill earlier of "Well, you are just going to have to live with it." That did not show consideration of your feelings or caring for you.
2. I do not like the lying about her having met with Bill because she didn't want to hurt her. She means, she didn't want the knowledge of her having more contact with him to hurt her.
3. I do not like hearing about her refusing to allow Bill and you to meet directly. This was a sign in my own prior marriage of trouble. If you want harmony in your life, there is no place for divisiveness. And Samantha's position on this one is extremely divisive.
I have a hunch that Samantha may love both Bill and you. But she lacks the honesty and candor to pull off a successful polyamorous relationship. I have no idea at all if Bill is playing a long game. And I don't think emotion coming into the relationship is inherently bad or even unexpectable. It is unreasonable to expect a woman to have sheet-ripping sex with a man several times a week and not develop loving feelings for the man. So, let's just assume she does.
What Samantha lacks, from my perspective, are the skills to make a poly relationship work. She is pretending this is a polysexual relationship when emotionally it is much more.
A successful polyamorous relationship has no place for deceit, "protective" lies, or divisiveness. The cardinal words for one include "open" and "compassionate" and "loving." Samantha doesn't seem to get it.
The other option others here have not mentioned would be to make a contingent stand about Bill. Either she needs to learn how to do this in a loving way that takes into consideration your feelings and her presumed love for you or she should end things with Bill. Have her read The Ethical Slut. If you folks have the resources (and it sounds as though you do), see Dossie Easton in San Francisco for some therapeutic consultation. Or Kathy Labriola in Berkeley. They are long experienced in helping people navigate poly relationships.
If Samantha is as smart as you say, then she can rise to the occasion and have both Bill and you. But she is sabotaging what could be a good thing. She is trapped in her own compartmentalization. That strategy may have worked for her in other life endeavors, but it is failing her in this one.
Really, my best wishes for you and her. Do work on what works for both of you. And it does not sound as though this is working well now.