1)digital optical port out for pass thru audio from MKV files, and an HDMI adapter hooked to the mini display to provide the MKV video out to an HDMI port directly to the WS TV.
With my particular AVR, the 3 HDMI ports allow HDMI, analog, optical. This means that an older MBP like mine needs the 2 separate outputs Video to the WS HDMI and digital audio to an optical input on the AVR. Thats why my connections seem a bit convoluted.
In your case, the mini display with adapter, I understand some adapters dont pass audio so get a name brand one, will enable you to use the one HDMI cable to an input on your AVR and you will be GOOD TO GO.
For many months, I sent the movies either from my iPad or from iTunes via wifi to the atv2. The most obvious thing is that you CANNOT get DTS sound this way. The ATV2 will downmix it to Dolby, a good dolby, but NOT dts. Using the direct connection like you envision and like I do now ensures DTS and excellent 5.1 A good AVR will also know how to create some sort of surround with most any movie with lesser tracks. I KNOW the sound is better what with DTS and unprocessed 5.1 tracks. I am convinced the video is better also, but that is of course subjective. I dont use full MKV files. I create them with HB set to 1792 or 2048 and have done higher like 2560, but not sure its worth the size. 1792 or 2048 sure seems good and gives about 74 to 78 % of the original video and of course ALL the audio. Good Luck.