I am mainly a Mac and ROCK user, so apologies in advance if my Windows knowledge is limited.
Dolby Atmos - you are 100% correct that Virtuoso doesn’t include an Atmos decoder. To my knowledge, the only headphone processor that includes Atmos, DTS-X and Auro decoding is the Smyth A16 Realiser (which provides up to 24 virtual speaker channels). Having compared both the Smyth and Virtuoso on stereo, 5.1 and 7.1 music and movies, there is a significant difference especially in bass quality and precision of speaker location, but Virtuoso is still great value for what it can do.
However, I haven’t personally found Atmos music (from Apple Music) to be super impressive - it seems to be lossy and/or upmixed. Movies are a very different matter, as Atmos can transform your entire experience. I have also played ripped Atmos blu-ray music through Virtuoso, using the 7.1 SMPTE layout (which has the classic F C R speaker location) with good results. The Virtuoso manual gives a lot more detail on alternate speaker layouts so you can experiment.
MKV - I have only played MKV movies, not music. So I can’t advise on this. I have transformed all my multi-channel music ripped from SACDs into FLAC files, and these play fine, alongside the limited multichannel FLAC streams from Qobuz.
HRTF - I believe that the Genelec HRTF costs around £1000, just for the measurements. If you are prepared to spend that kind of money, you could consider buying the Smyth A16 Realiser ($4,000) rather than Virtuoso, as it has full HRTF personalisation and room/speaker measurement capabilities, and is the go-to headphone virtualisation tool at many studios, including Dolby themselves. I also own an A16 Realiser but use Virtuoso when travelling. It’s a big investment, so check the Head-Fi thread https://www.head-fi.org/threads/smyth-research-realiser-a16.807459/ if you are interested.
Virtuoso works best with a headtracker, and preferably some ability to modify the HRTF response for individual ears. Most people recommend the £80 Supperware tracker (which I use), but then you are restricted to the 5 standard HRTF options in Virtuoso. Another option is Earfish https://www.earfish.eu which used to enable you to maker a custom HRTF. However, Earfish now seems to have been restricted to academic research users. The third alternative is Waves NX https://www.waves.com/hardware/nx-head-tracker which also has some HRTF personalisation options.
Hope this helps. Good luck!