The answer to your basic question is that in both methods, you are using the Marantz' DACs because the HDMI interface is conveying digital information and bypasses the DACs in the Oppo.

In addition, using the Oppo will also let you play multichannel files, via HDMI, through the Marantz, something that the USB input on the Marantz will not permit.

I may have spoken too soon because I have not tried any MCH with the 93 but only with the 103/105. Still, I know that the Marantz will not, but there is hope for the Oppo.

Kal;
Should my OPPO-105D be left on continuously for best sound? Is there an optimal warm-up period after turnoff ?

??? Try it. If it makes a difference to you, you have your answer.