Ya, right now I pop in a disc if you really want to have the HD audio track, so it's a bit of a compromise. I kinda let it slide since I have two young kids and don't raise the audio volume too high most of the time. Plus I focused more on getting the Disney stuff on the server for easier access and just key favorite movies for now. So it's not too bad, but ya, when I want uncompressed audio, I have to pop in a disc.
As for how it works, it really depends what the audio track is that comes with the Blu Ray. Fortunately most movies are DTS-HD MA which is backwards compatible to DTS so you don't have to do anything. Just rip it and it'll figure out which track to use. If it's Dolby True HD, then it comes with a separate track for the standard Dolby Digital 5.1. I believe it's in the spec that True HD has to include a regular track. I tend to rip all audio tracks so they're at my disposal and in the future or whenever I turn on the more powerful HTPC, it's available. Now if it's just a PCM only track, then you're kinda out of luck but even then I could have sworn any disc with a PCM track also had regular Dolby Digital or DTS at their disposal as an alternate track. Either way you should have options, but DTS-HD MA makes it the easiest.
Ya, there's ALWAYS a drawback and you just have to figure out what is the least painful thing to do without. For me, as much as I want HD audio, that only applies to movies. For streaming and normal TV stuff, it's a non issue. So for me, every day usage I find having all the various services like Netflix, Amazon and HBO being integrated by far more useful. It's also way easier than it ever was before for the rest of the family to use since it's all integrated. I hear you on HBO though. For me it was Disney which was blocked by DirecTV. Fortunately, they finally opened that up. Hopefully HBO Now might let you bypass Comcast once the exclusivity is up.
Before, my HTPC was only for media stored on the server and Netflix sorta worked because of the Windows Media Center version being somewhat friendly to working. But nothing else did easily. As for the other services, forget about it. So to some, I'm sure it sounds surprising that I went away from a $1000 gaming HTPC and switched to a sub $100 Amazon Fire TV. So ya for me, easily going between everything that was remote friendly and easy for the rest of the family was a huge deciding factor. I still can do the other stuff, but since they are less frequently done, I just use either the HTPC or Blu Ray player when I want to do those less frequent tasks.