It sounds to me that she is slowly loosening her grip on what she's comfortable with when she's not around. Since there's a history of Tom cheating it sounds to me that she's still working on regaining trust in him.
It also sounds that things are moving forward, not stagnating or moving backwards. There's something that is said here a lot of the time of moving at the pace of the slowest person in the relationship. As time goes on I expect that more and more of the restrictions on you and Tom will be lifted.
It sounds to me that you are all talking together and are committed to working things out between the 3 of you.
Everything will be ok in the end. If it's not ok it's not the end.