At one point I had 8 consoles modded with borti's 32khz digital audio boards, 4 Mini's and 4 fat 1CHIP's. Some were toslink and some were coaxial, each using a DIT4096. When testing out on my receiver, a Yamaha RX-V477, all 4 1CHIP's worked perfectly fine with no dropouts at all. When testing out the Mini's, all 4 had an obnoxious amount of audio dropouts. I took a short video at the time to showcase the issue. I didn't get any audio dropouts with a cheap PROZOR DAC but with this receiver it was awful. I had followed the installation method shown on RetroRGB's site since it was easier to use those vias rather than solder directly to the S-APU pins. Some pics of one install:


Despite having a clean install, the dropouts randomly occurred every 3-20 seconds or so. Why were the 1CHIP's working without issue but Mini's having dropouts? I couldn't for the life of me figure out why this was happening given that my installations were clean along with the fact that Mini's and 1CHIP's are essentially identical consoles. I reached out to L-Train for help. He suggested the variance in compatibility might have to do with the difference in location of the S-APU between each console. On Mini's the S-APU is located near the front of the console and on 1CHIP's it's located at the back. With Mini's, most people will grab the digital lines from the vias and route them to the back of the console. When doing so, the digital input lines are too long and become compromised. This isn't an issue on 1CHIP's since the S-APU is located near the back of the console hence the digital input lines aren't nearly as long. Because of this he suggested that I try mounting the digital audio boards of the Mini's closer to the S-APU and wiring the output to the back of the console instead, which I did:

In one console I mounted the board directly on top of the S-APU as I wanted the digital input lines to be as short as possible. I hooked it up to my receiver for testing and I went 2 hours without a single audio dropout. I then redid the other 3 Mini's and tested those consoles 2 hours each. In total 8 hours of play and not a single audio dropout. At this point I was confident in saying that mounting the board closer to the S-APU completely solved the audio dropout issue. All hail L-Train.
This isn't a callout or personal attack by any means, as I'm simply trying to help people who might be experiencing compatibility issues, but the digital audio installation method for SNES Mini's shown on RetroRGB's site, in my experience, will yield suboptimal results. The digital input lines are too long and become compromised. I suspect that most cases of users experiencing compatibility issues has actually nothing to do with the quirky sample rate of the SNES but rather compromised digital input lines. What also came to mind was this has been the go-to method for digital audio installs in SNES Mini's for some time now so that can only mean there are many Mini's out there with improperly installed digital audio mods. I can't guarantee that this method (mounting the board closer to the S-APU) will resolve all compatibility issues as I haven't tested every DAC in the world but it certainly fixed mine. In fact, with this method, every 32 khz compatible DAC that I've tried has worked flawlessly, including:
-Monolith by Monoprice Desktop Headphone Amplifier and DAC
-Monolith by Monoprice Portable Headphone Amplifier and DAC
-Topping DX3 Pro
-SMSL SU-8
-Parasound Zdac v.2 DAC and Amp
-PROZOR DAC
-Yamaha RX-V477
With regards to my Topping DX3 Pro, it is listed as supporting 44.1 to 192khz only, yet it works fine with borti's 32khz board when I turn off the Auto-Off feature. On a sidenote, the Topping DX3 Pro is one of the best bang for your bucks in audiophilia at the moment, for those that dare to go down that rabbit hole, although I recommend waiting for the revised unit that should soon be out.