Sorry to ping a two month old post, but I've found a workaround to get VR mode working through SteamVR!
1st, Go to steam on your computer, click "Games" in the top left, then "Add a non-steam game to my library".
2nd, Select any .exe program from the list it provides you. Any .exe will work, but I'll use Microsoft Edge for this example. Once you've selected one, make sure to click "Add Selected Programs".
3rd, Scroll through your Steam library until you find the name of the .exe you chose (Microsoft Edge in my case), right click on it and select "properties".
4th, In the TARGET field, click "Browse" and navigate to where your version of HypnoGen is on your computer. Make sure to change the file type from "Executables (*.exe)" to "All Files) in the bottom right. Click HypnoGen-VR and then click "Open" in the bottom right. Once that is done the file path should be in the TARGET field. Make sure to add qutation marks (") to the beginning and end of the file path.
5th, In the START IN field, click "Browse" and navigate to the same file that you found HypnoGen-VR in. Click "Select Folder" in the bottom right once you're there. Check the "Include in VR library" box at the bottom to make it easier to find, and you can change the application name at the top from whatever .exe to HypnoGen or any other name you want.
It should now start from within SteamVR and run like normal.