This is exactly the point.
And it's baffling to me that a AV receiver's DSPs have no problem rendering 11 channels at 48kHz 24bit, and apply bass-management plus realtime room-correction EQ etc; yet when there are much fewer active channels (e.g 5.1 in my case), and on one of which I want to apply only some simple EQ eg. the center channel, then it still truncates a 96kHz flac down to 48kHz.
There is lots of horsepower in any modern AV receiver, but clearly most of it isn't being used -- unless you have a Yamaha-built unit it seems.
I don't think Yamaha made their own DSP processors and it is hard to imagine D,M,O and others would go with less powerful ones to save cost either. So with the ever increasingly more powerful processors, manufacturers are probably just too lazy or didn't feel there is a need to change their design when they know/think there is no gain in doing so, plus they know full well the vast majority of their potential customers don't know or care much about whether the REQ software down samples or not. They don't tell you anyway in their marketing information. Even Yamaha, you think they would highlight their YPAO could run on loss less files without down sampling to 48 kHz on their website, but they wouldn't bother, unless I missed something..