True, but the HD audio over analogue is only uncompressed because the Blu-Ray player has decoded it. So if you have Dolby TrueHD or DTS HD signal on the Blu-Ray disc, the Blu-Ray player decodes (or uncompresses) it and sends it to the amp. With the signal bitstreamed over HDMI, it's the amp that decodes it. So either way, in theory, you're still getting the same sound.
However, I've found with the PS3, if I let the PS3 decode a standard Dolby Digital / DTS signal and send it as PCM via the HDMI cable, it doesn't sound as good as if I bitstream the same Dolby Digital / DTS signal via the HDMI and let the Onkyo amp decode it. In theory therefore, the same should be true of the HD audio formats as well. Of course, I can't test this as the PS3 doesn't let you bitstream HD signals via the HDMI port!