As a Japanese person, if some one says this to me, I would think, ‘Oh shoot, what did I do wrong?’ To me this has the nuance of, ‘Please, I want you to treat my house like how you would want your house to be treated by guests.’ I think I get this vibe from this sentence because of the word 扱う, since that word means to handle or to take care of. The use of that word makes it sounds like they are prioritizing the house and not you, if that makes sense.
Personally, I would never use this sentence for hospitality purposes since the person I’m saying this to might assume that they did something wrong. I would probably say something like, 気楽にしてね, or be more direct and say, 遠慮しないで、勝手に冷蔵庫のものとか食べたり飲んだりしてもいいからね。