The distance of the two cameras inside the virtual environment doesn't matter that much. In fact the two cameras can even overlap or be twice the distance they should be inside Unity / whatever platform your using. Moving the cameras side by side just amplifies or diminishes the stereoscopic effect.
The 65mm / 45mm refers to the distance the center of the two cameras in the real world. The best way to illustrate this is with a simple photo rather than a 3D environment.
Here is an image to illustrate this. Please note: if you just use the same image SBS, the distance between the center of the two images is at 65mm. And it has to be at 65mm regardless of how big the screen is.
Now the problem is that this rule would work fine if the center of the lenses would be exactly where the center of your eyes is. Otherwise you also have to deal with a shift of the image that happens in the process of magnification / distortion. This shift will be towards the center of your phone if the distance between your eyes is higher than the distance between the 2 lenses, and outwards if it's the other way around.
So for example, on Altergaze the distance between the two lenses is 52mm. So if the person viewing the screen has an IPD of 65mm, then the distance between the two images on the screen needs to a bit lower than 65. For an IPD of 45mm, because the image shifts outwards when magnified, the distance between the two images on the screen needs to be a bit higher than 45.
If you want to approximate it I would just use 50mm (instead of 65mm) and 47mm (instead of 45mm). This is for Altergaze of course, for Cardboard where the distance between the two lenses is different, the shift will be different. The magnification value of the lenses also affect on how great the shift is.
Hope this makes sense. I wrote a long article about the way I calculated the stereoscopy in relation to the screen, but never published it
I have to go over the math again and do some more tests. I will do so in the next couple of weeks before making the SDK public and include all this information with it.