The documentation for $in/$all only mentions that it works with straight values:
http://docs.mongodb.org/manual/reference/operator/in/#op._S_in
http://docs.mongodb.org/manual/reference/operator/all/#op._S_all

It seems to work fine with $elemMatch which is a very common use case, e.g.:
http://stackoverflow.com/questions/9824341/multiple-elemmatch-expressions-for-matching-array-values-using-all-in-mongodb

Also $in works with $regex at least.
We should list the operators that are accepted within the array of values.