Hi GLC650,
I know I’m really late to this topic, but I may have some insight to offer. I too have a Topping D90SE (awesome, by the way) it is connected via USB to my Roon Nucleus Ver. B. As it stands, I didn’t even notice that all of my file formats, except DSD were displaying as PCM. The sample rate (e.g., 44.1 kHz was always spot-on), but I wasn’t getting MQA format through the D90SE. What I discovered is that I had to turn off all DSP filters, including my Audeze preset. The D90SE is setup as follows:
MQA Capabilities: Decoder and Renderer
Enable MQA core decoder is set to yes/on
This configuration provides full MQA playback. I tested my new settings by listening to 
, which showed up on the D90SE as MQA 352.8kHZ. I can’t say for certain, but it is possible that MQA is an iteration of PCM, which is why the sample rate is spot-on. Anyway, I hope this helps.
Cheers!