> English is the only language where I hear such illogical statements.
Fear not, the exact same thing happens in other languages. Must be that you just don't hear much, for instance, Swedish: "Allt som glittrar är inte guld." (Should logically be "Inte allt som glittrar är guld", just like in English.)
> Same goes for the inverted usage of "all but", which imo _should_ mean "everything except for" but seems to mean "almost". I wonder what causes this.
That doesn't feel "inverted" at all to me. You just need to interpret the "all" as it must have been intended: "the whole"; "all the way there" -- then "all but" quite logically becomes "not quite the whole way there".
Like, if a piece of software was almost, but not quite completely, finished ==> "the software was all (the way to) but (not quite arrived at) finished."
Maybe it helps to see the similarity with this related form: Almost all the bugs were fixed, but one was left ==> "All but one of the bugs were fixed." (The bug-collective was all but vanquished. :-)