Your Sony Home Theater System probably doesn't support FLAC because it doesn't have the codec to uncompress the FLAC audio files.
It kind of depends on the features of your hardware and the settings on whether you are getting the best audio output.
Most likely, this is what is happening:
Your laptop is decoding the FLAC file to an uncompressed digital format.
The digital audio is sent to the TV through the HDMI cable.
Depending on how you connected your TV to your Audio Receiver:
3(a). The TV converts the digital audio to an analog signal that is sent to your Audio Receiver via RCA connectors (the red and white cables)
3(b). The TV passes the digital audio to the Audio Receiver via an optical cable, a digital cable, or another HDMI cable. Then the Audio Receiver converts the digital audio to an analog signal.
- The Audio Receiver amplifies the audio signal and sends it to your speakers.
Step 3(b) is probably better than 3(a) because the Audio Receiver will usually convert an analog input back to digital for Digital Signal Processing (DSP), then convert the digital signal back to analog for output to your speakers.
For stereo music stored in a FLAC file, I think you are getting great sound quality. If you are playing 5.1 audio from a DVD or BluRay, there could be some compromise on the audio quality. It's very possible that your laptop or your TV will only send a stereo (2.0) signal to your Audio Receiver. The reason why you are hearing sound from all your speakers is from the DSP that your Audio Receiver is applying to the audio signal.