Good Day:
The quick answers are no Sony plays back DSD 1x, yes there is one pop on start of playback and one pop if you next put in a CD when it switches back to PCM.
The OPPO and Sony DSD output are the same sound quality differences minor if at all.
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More Detail
The thumps were during shutdown via HDMI while DAC was on with Oppo 83se with this unit there is also sounds when switching audio. So going from intro to fbi warning to main menu on DVD-Audio and DVD movie disks. Same experience with Toshiba HD-A30 (HDDVD player have 50 movies). Both work fine into my Marantz SR7012. Which it also turns out can play SACD disks at DSD 64 (1x) no pop, but SQ

. The Oppo I have to power cycle with AC Cord to get HDMI input light to go from red to blue hence thuds unavoidable (everything is triggered) also a POP when light goes from red to blue as it boots up and starts to play SACD. So handshake issue not expecting it to be fixed the OPPO and Toshiba are 10 years old. The Toshiba also can't output audio over HDMI have to use Coax SPDIF with Marantz yet it works with BDA-3 except switching noise (ahhh standards...)
With the Sony UBP-X800m2 I get a thump when shutting down so plugged it into always on and let it's power management shut it down when I am not listening to it or stereo has shut off. The BDA-3 has it's own HDMI output to TV completely avoiding the Marantz so I can still do 4k. So with Sony outputting to BDA-3 on an HDMI input I get 1x DSD light is blue, same if I check Bryston inputs webpage it also reports Single-rate DSD (what you click from My Bryston page). In the Sony Setup the only DSD setting is Auto or off. Off plays PCM 16/44. I have tried ARC on and off no difference and leave it off, HDMI CEC is a nightmare.
The other setting in audio settings on Sony concerns bitstreaming or PCM and has no affect on DSD. That being said DSD 1x is 176.4 if it were converted to PCM. That is not happening and staying as DSD which is what I want. There is also a POP as Sony starts to playback DSD 1x assuming you weren't listening to DSD already. Interesting to
Note until SACD playback starts the blue light is on for 176.4 which POPS then changes to DSD 1x.
As mentioned when playing Native DSD (light is pink/Amber) from files I get POP and only as playback starts, after that no problem until you switch away again to another format such as PCM.
I am not an expert but get feeling this is
switching noise as it switches from PCM circuit to DSD circuit and back.
Stay safe
PS the sound is amazing, while PCM is a bit better than my RME ADI-2, DSD is leaps and bounds ahead, so hope for a fix. By far Native DSD with ROON from a Windows computer (ASIO drivers) as ROON bridge sounds best. I found the same RME (Asio drivers) sounding better than PCM. The BDA-3 being the better of two.