What is the desired change here, given that zlib does not support this? The current behavior seems appropriate here.

Maybe you should give a warning when trying to initialize compression with a window size of 256 bytes and warn that a 512 byte window is actually being created.

Test script:
---------------
$filename = tempnam(sys_get_temp_dir(), 'zlib');

$expected = 'foo';

// write to file the compress content
$context = deflate_init(ZLIB_ENCODING_DEFLATE, ['window' => 8]);
file_put_contents($filename, deflate_add($context, $expected));


// read content from file and uncompress it
$context = inflate_init(ZLIB_ENCODING_DEFLATE, ['window' => 9]);
$actual = inflate_add($context, file_get_contents($filename));

var_dump($expected === $actual);

Actual result:
--------------
bool(true)

In my opinion, this is merely a documentation issue on our part.

I agree. It will be great if you document this bug.