"He does not agree with himself."
Translation:Anh ấy không đồng ý với bản thân.
That would mean "he doesn't himself agree" and it sounds quite weird as well. The last sentence you gave uses "tự" to mean "by themselves". So whenever you see: "X tự Y bản thân" it means "X are Ying by themselves, to themselves". "Tôi tự giúp bản thân" = I myself help myself.