Your signal path is showing the MQA is being decoded by the Topping not by Roon. To break it down:
the audio is being received by the Mac-Mini from Roon.
The mac Mini is sending the audio to the D90SE via CoreAudio in exclusive mode
The Topping D90SE is decoding the MQA.
As you have turned off all MQA decoding in Roon, only the Topping is doing the decode. If you want to turn that off, then you would have to go into the Topping setup.