FLAC is no problem. You won't be able to get DSD from a PC into any device over HDMI; the video cards don't support it.
If you're addicted to DSD, for direct playback you either use the SACD player or get a standalone USB DAC. You could also get DSD into those devices via DLNA or a USB storage device, but 2 channel only. I don't recommend DLNA.
In my opinion, (when you're talking about those specific devices, the top of the line processors, and yes I've had them in my house) the Yamaha sounds better than the Marantz. More musical, more natural. It also runs a lot cooler, which matters if you're going to keep it in a cabinet or stack. The Yamaha also lets you select different filters for the ESS DAC, if that interests you.
There are DACs that can sound better, but you have to listen carefully and shop carefully, and the selection of high quality multichannel DACs is extremely limited. But there is an issue of practicality. DACs just don't do the things that processors do. A Ferrari drives better than a BMW, but it's pretty useless for taking your 3 kids to school. Or bringing anything home from the store. Etc.
If you want the absolute best audio quality and don't need any functionality other than listening to a single audio-only source, get a DAC. If you need to do anything else at all, get a processor. The Yamaha sounds great.
MC hooked directly to a processor with HDMI is a great solution for multichannel audio and video.
You have to decide for yourself what pleases you. Do your research and do some listening.
I hope this helps... Good luck.