Once read alll the RFC 1950-1952, checked the zlib manual, read here and there the C source that implements zlib.deflate, and having experimented myself (see bug #71396 for a test program), I finally came to the conclusion that explains why the example#1 cannot work, and why that manual page needs a deep update:

http://php.net/manual/en/filters.compression.php

I'm not a doc contributor, but the following text might be a start:


zlib.deflate: what it really does and what the 'window' parameter really means
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The zlib.deflate filters implements the compression methods DEFLATE, ZLIB and GZIP depending on the value of the 'window' parameter.

The 4 lower bits of the window parameter set the size of the internal “history buffer” used, being the base-2 logarithm of its size in a range from 8 up to 15. The meaning of the others bits of the window parameter can be set as described below.


- DEFLATE (RFC 1950) is a raw compression algorithm without header, without checksum. It is performed when the window parameter is set in the range from -8 up to -15. This compression algorithm is the base for all the formats generated by the zlib.deflate filter.
The corresponding functions that operates directly on string are gzdeflate() and gzdeflate().


- ZLIB (RFC 1951) applies the DEFLATE algorithm and adds a 2 bytes header and 4 bytes trailer containing the Adler32 checksum of the uncompressed data in little-endian byte order:

        ZLIB = ZLIBHEADER(2B)  DEFLATE  ADLER32(4B)

The 2 B header, read as 16 bit unsigned number in little-endian order, must be multiple of 31.
This format is generated when the window parameter is set in the range from 8 up to 15.
The corresponding functions that operates directly on string are gzcompress() and gzuncompress().


- GZIP (RFC 1952) applies the DEFLATE algorithm adding an header and a trailer with the CRC32 checksum of the uncompressed data and their length, both in little-endian byte ordering:

        GZIP = GZIPHEADER(10B)  DEFLATE  CRC32(4B)  LENGTH(4B)

This is the format of the .gz files, with the GZIPHEADER containing in the order the GZIP signature (“\x1f\x8B”), the compression method (“\x08”), 6 zero bytes, and the operating system set to the current system (“\x00” = Windows, “\x03” = Unix, etc.).
This format is generated when the window parameter is set in the range from 8+16=24 up to 15+16=31. Note that there is a limit of 4GB to the maximum length of the compressed data; beyond this limit, only the modulo 2^32 of the actual length is stored in the LENGHT part.
The corresponding functions that operates directly on string are gzencode() and gzdecode(); the gzopen() function allows to read and write .gz files.


By default window=-15, so generating a DEFLATE compressed stream with an internal history buffer of 2^15 B. Invalid window parameter may be detected and a quite obscure error can be generated:

       E_WARNING: unable to create or locate filter “zlib.deflate”


All this explains why the example #1 does not work and nothing can be read back. In fact using window=15 it generates ZLIB which the following readfile('php://filter/zlib.inflate/resource=test.deflated'); statement cannot read because it is expecting DEFLATE. The same example works setting the default window=-15.

The remaining big question is why the original example#1 does not work but no error is shown. But this is another story.

Completing description with the zlib.inflate filter:


zlib.inflate filter
-------------------

Only the 'window' parameter is allowed; any other parameter (memory, level) is ignored. Be $W the base-2 log of the history buffer size, so that 2^$W bytes are allocated by the decompressor. This value must be greater or equal to the value used for compression, because no attempt is made to reallocate. The range is 9 <= $W <= 15. If unknown, $W=15 is the safer choice.

- DEFLATE (RFC 1951): use window=-$W, with $W being a value not less than that used for compression. If unknown, set window=-15.

- ZLIB (RFC 1950): use window=$W. The value of $W is available from the same ZLIB header, otherwise set window=15.

- GZIP (RFC 1952): use window=$W+16. The value of $W is available from the same ZLIB header, otherwise set window=31.

- ZLIB or GZIP: use window=$W+32 for automatic header detection, so that both the formats can be recognized and decompressed; window=15+32=47 is the safer choice.


Error detection:

- If the window parameter is not one of those listed above, an error MAY be generated:

	E_WARNING: stream_filter_append(): Invalid parameter give for window size.

- If the $W value is less than that used for compression, an empty string or a short read MAY result, but no error is triggered nor exception is thrown. This last issue reveals when highly compressible data (say, a source program at least 40 KB long) that were compressed with large window (window=15+16), are then decompressed with a smaller window (window=9+16).

- On checksum fail, corrupted or incomplete data are returned, but no error is triggered nor exception is thrown.


(About the missing detection of decoding errors, see bug #71417.)