I've seen the back and forth on this for a while. The two camps are: Those who rely on data only, that say nothing should be different. Those that have experienced a difference. I am in the latter category. I know The former camp will curse my name and tell me I don't know how to level match and all that, but I trust my ears, and, even better, I have a theory.
See, technically, it should be the same. So let me theorize how it might not be. It's not a matter of post-processing, since I run my receiver in Direct mode. I don't like filters of any kind. It's not even the PCM format. In fact, my favorite disk is CARS with a PCM track that is killer. But what happens is when material is decoded I think the decoder makes a difference. If my player (LG BH200) decodes, the sound is relatively flat and less dynamic with less detail (almost like it was still compressed) compared to when my receiver (Marantz sr7002) does the work. Now, here's where my knowledge breaks down, because I cannot tell you why this happens. I can only blame the player, not the process, because the process is done correctly in my receiver. I know that some software on my computer can sound different than others, even running the same video. I've also heard the PS3 decoding sounds crappy compared to a stand-alone player (how is that possible if decoding is all the same?) So I blame the product that is decoding, and that explains (perhaps) why the receiver is the best bet for proper HD sound decoding. It doesn't mean there won't be players out there that sound as good as any receiver, it just means there are some players that don't. Optimally, a superior player will decode into beautiful PCM and be able to add secondary audio such as commentary. For me, I am happy with bitstream as it gives me the best sound out of this player (I am very picky about dynamics and detail). So, I'll keep it until I'm forced to get another player to keep up with many changes in blu-ray technology.
Note: my player cannot correctly decode 6.1 or 7.1 channels. If those channels are present they are mixed into the 5.1 and sent by PCM. Bitstream of course is fine. If something like this can happen, where the purity of the original is diminished, I think it's plausible to say that the quality of sound can be lost through improper decoding as well. In fact it may be this 'mixing' of channels that adds a kind of filtering stage to what should be a pure sound, and that MIGHT be what I'm hearing. But that's just a total guess.