Oh lastly the drive cage in the Lian Li Case can be removed which is what I would do to increase the cooling effect of the front fan. Instead of cramming the case full of HDD which would be better served in a proper nas box or Windows Home Server.
I'll reply to this one other than wall-of-text quoting..
The motherboard can hold a discrete GPU! It's all about the case.
BitFenix Prodigy would fit nicely, but those Lian Li's sure are sexy.
SilverStone also make some incredible ITX chassis like the FT03 that would house a GPU with no issues.
I just got done playing around with an ASUS P8Z77-V PRO, but I use an ASRock Extreme6 for day-to-day. Very similar boards - I prefer the ASRock though, for one of the reasons you list above: mSATA. I also prefer the fact the ASRock has a debug LED whereas the ASUS has the phase LEDs.
Yes the prodigy is a nice case and so is the silverstone but like you said Liang Li just has that appeal. Plus I know the mobo and case can accommodate a gpu, but I don't want one for the reasons I said above. I'd rather have the tv tuner in there.
I built my dream rig a little while ago. It had at least 24 gigs of graphics on it... I can't remember the exact specs but it probably had 128gb RAM XD It was an absolute BEAST! Only NASA could afford it, though. It all came to around 34.5k... XD I wish I had that money floating around.