Something something “don’t make me choose, Shiv, it’s a man’s right not to choose” but then choosing to leave work on his first day more than once to be with Shiv (despite knowing that this is going to hurt his workplace rep). something something Shiv refusing to actively choose to sacrifice Kendall on the yacht and yet still implicitly choosing him by refusing to sacrifice Tom. Neither of them are willing to make sacrifices boldly, both of them are trying to hedge their bets and play the field, but up until season 3, when the rubber really hits the road - when there is no way to choose both at once - they do choose each other.
Tom is the first to stop choosing Shiv, but he does it only after believing that Shiv won’t choose him, hasn’t been choosing him, even as - in his mind - he keeps giving her opportunities to choose him and she doesn’t. Shiv doesn’t realize that the choices she’s making are in fact choices. If Tom wanted something from her he would tell her, she thinks, not realizing that for Tom asking for those things is his own vulnerability, and he can’t ask for them in the same way she can’t express her own fears and desires and vulnerabilities. So she doesn’t choose Tom - but she also never consciously stops choosing Tom in the same way Tom stops choosing her.
On the one hand, Shiv would never betray Tom in the same way Tom betrayed her - but on the other, in Tom’s mind, she already has. The wedding night is a betrayal, accepting the CEO position is a betrayal, not standing up for him on the yacht is a betrayal. If she loved him she wouldn’t have done those things, if she loved him she would have seen how upset he was, if she loved him she wouldn’t have forced him to say it out loud. Each of those is, to him, an immense betrayal, two of which specifically involve choosing Logan over him. Is his betrayal really all that different? Of course, Shiv doesn’t know these are betrayals. The idea that to Tom, these are not just wounds, but fundamental betrayals of the very foundations he believed their relationship was built on, never once crosses her mind; and for his part he can never really tell her, not in those words. To admit just that he’s hurt is painful enough. So she goes to Logan for him, and she thinks that this has settled the score, that Tom understands now that she loves him, and she doesn’t realize that it hasn’t, that she needs to prove that she does love Tom enough to undo the pain of those betrayals or else her entire marriage will fall apart. (And even if she did know - could she? Is there really any length she could go to that would undo those hurts? Can the ‘score’ ever really be settled, or is she facing an audition she could never possibly win?)