There's a good chance you'll pull your hair out trying to get bitstreaming from an HTPC working correctly. Other than it being very expensive (you'll either need a GPU that supports bitstreaming, or an external soundcard (Asus HD Slim), then you'll need a new-ish amp that supports the new HD audio formats. Then there's the issue with some receivers not supporting the correct EDID options for 5/7.1 surround. It goes on and on. There's also the issue with supported software. While both PDVD and TMT3 now support bitstreaming, you need the 'full' (expensive) versions of both, and an audio card that supports PAP. This is also the only way to get full HD audio out of these that's not downmixed to 16-bit/48Hz either.
I've used FLAC in an MKV container from the beginning, actually sent over the 5.1 analog outputs from a cheap Asus Xonar DX to the analog inputs on my receiver (any recevier with analog inputs will work). The audio is sent full bandwidth, and sounds fantastic. No reason why you couldn't do this over HDMI as well, but in my case, the HDMI connection from the HTPC goes straight into the TV. This way, normal viewing uses the TV speakers, but switching to MPC-HC for HD rips uses DirectSound over-ride to send audio to the Xonar DX. All seamlessly launched from within MediaBrowser.
And honestly, for watching BD movies from disc, I have a blu-ray player, which means when I want it, I can get the audio bitstreaming to my amp anyway.