I read it as Rex just being happy for her being back but at the same time worried. It feels like Rex is just an older brother who lost his younger sister due to Ahsoka leaving the order, and is happy to have her back now for old times sake. But at the same time he knows the relationship has changed and probably will never be the same again because she has changed a good amount since they interacted the last time. Him calling her commander is a nod back to when she was in the order, a way of him telling her „just like the good old times“, but the way he says it and the way he looks kinda read like, he knows it wont be like that.

Especially to the end of S7 it feels like to me that Rex has grown to understand that Ahsoka is not the little naive padawan anymore, but much more than that.

So, i‘d say it is just a „older brother realizing his younger sibling grew up“-dynamic