I don't know why everybody tells me that FLAC won't work. FLAC does indeed use WAVEFORMEXTENSIBLE.
https://en.wikipedia.org/wiki/WAV#Description
Beginning with Windows 2000, a WAVE_FORMAT_EXTENSIBLE header was defined which specifies multiple audio channel data along with speaker positions, eliminates ambiguity regarding sample types and container sizes in the standard WAV format and supports defining custom extensions to the format chunk.
All the changelog says is that flac (the reference encoder) respects the WAVE_FORMAT_EXTENSIBLE header instead of just guessing the channel order. This doesn't change the fact that FLAC (the format) only supports a very limited number of channel orders. Also, the changelog for that is over 5 years old.
This is what happens when you try to encode a WAV with a WAVE_FORMAT_EXTENSIBLE header that FLAC doesn't support
$ flac a.wav
flac 1.2.1, Copyright (C) 2000,2001,2002,2003,2004,2005,2006,2007 Josh Coalson
flac comes with ABSOLUTELY NO WARRANTY. This is free software, and you are
welcome to redistribute it under certain conditions. Type `flac' for details.
a.wav: ERROR: WAVEFORMATEXTENSIBLE chunk with unsupported channel mask=0x070F
General
Complete name : a.wav
Format : Wave
File size : 288 MiB
Duration : 5mn 0s
Overall bit rate : 8 064 Kbps
Audio
ID : 0
Format : PCM
Format settings, Endianness : Little
Format settings, Sign : Signed
Codec ID : 00001000-0000-0100-8000-00AA00389B71
Codec ID/Hint : Microsoft
Duration : 5mn 0s
Bit rate mode : Constant
Bit rate : 8 064 Kbps
Channel(s) : 7 channels
Channel positions : Front: L C R, Side: L R, Back: C, LFE
Sampling rate : 48.0 KHz
Bit depth : 24 bits
Stream size : 288 MiB (100%)