Not setting is same as setting it empty. No bug.

Applications often make distinction between empty and not set.

Example:

Set filter to '': http://example.com/articles/?filter=
Don't change filter, get it from cookies: http://example.com/articles/

But of course, this could be wrong way of using this. Is suggested explanation 
part of some standard/specification?

Not set is not the same as empty:

http://example.com/?foo=&bar=2&hash=XXXX

$hash = $_GET['hash'];
unset($_GET['hash']);

if ($hash != hash(http_build_query($_GET))) {
    echo 'Hash mismatch';
    die;
}

Now we can't check the hash as http_build_query() won't return the

"URL-encoded query string from the associative (or indexed) array provided."

The original array is not used, a filtered copy was
processed instead.

This is, IMHO, a poor design solution because we sometime want to provide a clear value to a parameter... as said before, empty is not the same as not provided...

In 2022 this in still marked as NOT A BUG because someone did not understand the difference between "not set" and "empty"?

example.com?foo=bar (set value)
example.com?foo=    (set value to "empty")
example.com?        (do nothing)

The only solution to have things work like above is to rework this bad designed core php function every time? Won't be ever fixed?