I have searched a lot on the internet. I can save you time. One day as of this post Unity offers absolutely nothing to get a single render texture with stereoscopic view using Single Instance.

But of course, there is the issue that if you want to make a relatively complex game Single Instance is practically mandatory.

The only solution I have found is also quite simple: use two cameras for each of the eyes of the HMD viewer. So, for each stereoscopic texture that we want, for example a portal, we will have to create two cameras that will track the position of the eyes in a relative way, recording the texture in two render textures that we can assign to each of the textures of a shader that unify in a single vision.