Perhaps I don't understand your question, but why don't you try it both ways (with the DAC hooked up to the digital out on the Theta vs using the analog out from the Theta) and see which you like better.
Sidssp is correct. I agree with Michael, you could borrow a digital cable from a friend and compare them both, see which one sounds better to you. Very easy to do and completely reversible. I would be surprised if the difference between the Theta and the Marantz as transports would be as much as the Theta's analog stage vs. the MSB, but you never know in this hobby...
Well, I did an A-B comparison......and there is no comparison!!!
The MSB is absolutely NO MATCH for the incredible Theta machine. Adding the MSB Link DAC was like putting a VW motor in a Porsche Turbo body. MSB is in a totally different class.
I have to say I'm relived that my money was well spent on the Theta Miles.
Perhaps yes, perhaps no. You see when you separate transport and dac you introduce "jitter". You also introduce a number of other issues, like; power cords, additional shelving, proper isolation, cabling. Any one of these can take an otherwise great upgrade and render it blah. If you got a good Miles (apparently there are unit to unit sonic differences), look at upgrading elsewhere first, as you've done well.