Yes, when A/B testing the most obvious thing is that the audio coming from the Amiga's line out is a good deal louder than the audio coming from the monitor's line out. Perhaps there is enough headroom in the HDMI audio channels to allow for increasing the volume a bit without risking clipping the audio?
It also sounds a little (really just a little) different in a way that's hard to describe, but it's only reasonable that an 28-year-old 8-bit sound system is going to sound a bit different from a modern one.
Everything I tested sounded really good, especially Paul van der Valk's excellent Hybris soundtrack.
I also tested playing back MP3s using AmigaAMP using AHI.
The one thing I had an issue with earlier was playing MOD files in Protracker 3.15 running in a PAL screen and then switching back to a higher resolution screen. I think that was mostly/only an issue at 48 kHz, not or not nearly as much at 96 kHz. This now also works fine. (Tip: when you map different Amiga resolutions, such as PAL and DblPAL, to the same monitor resolution, the screen cycling doesn't trigger an HDMI reconfig so the display and audio don't blank out for a second. And if, like me, you're trying to use Protracker with a USB mouse and the RapidRoad, mouse clicks don't register, you need to click with the regular mouse.)
However, I did encounter something weird when I tried the above. My Workbench was in DblPAL, so I tried switching it to DblNTSC while Protracker was running in the background. Testing the screen resolution was fine, but then activating it brought up a blue screen with some gray horizontal lines at the bottom, with the Indivision reporting a completely different resolution. The audio was garbled. However, I was able to get out of this with Amiga-M, Further cycling through screens didn't return me to the blue screen.
Then it occurred to me that I run Copper-Demon, a utility that uses a custom copper list to create a background color gradient. After quitting Copper-Demon the issue didn't come back, but now I had a garbled mouse pointer after changing the Workbench screen resolution. But the mouse pointer returned to normal after switching screens. (The garbled mouse pointer also appeared on the Amiga's analog output, though.)
However, I couldn't reproduce this after a reboot.