Audiobear,
I did just what you suggest and have my CD67SE both Analog and digital into my 990. And the compared the 2. They are very different to my ears anyway. As for better? Can't say, but different. On some CD's the analog sounds better, on others, the digital. BTW the analog is done with 990 in bypass.
My preference right now is either bypass or digital upsampling. I'll probably end up with the digital mostly for convenience (set it and forget it).