1: He can but wait. : he can only wait
2: He can not but wait. he can not do anything else, only wait
Usually you will find it without a gap: He cannot but wait. This is a bit more archaic or poetic, but with a gap it looks awkward .
The structure "He can not but..." "He cannot but..." "He can but..." "He can not help but..." all mean the same thing, that there is nothing else he can do. There is no logic to this, it is just a common phrase (slightly archaic now).