If you shoot a movie for one screen size you'll not be able to obtain the same perceived depth on another display by only modifying the separation between the two images. There is an interesting article on the Siggraph website that illustrates the problem of varying screen sizes for stereo 3D : Stereoscopic 3D Film and Animation - Getting It Right

I've put up a little table to help me understand the situation better, feel free to comment if you find anything wrong in it.

For example, if you've got a movie with a maximal separation of 65mm on a 65" display, it will have a maximal separation of 40mm on a 40" display. This means that a point perceived 100m behind the screen on the 65" display if viewed at 2,6m (maximal distance for visual acuity¹) will be perceived at 3,90m on the 40" display when viewed from the same distance. If you look at this point at the best distance¹ of 1,6m for the 40", the perceived depth will be of only 2,40m.

If you augment the distance between the two images to have a maximal separation of 65mm on the 40", and watch the same point from the ideal distance of 1,6m, the perceived depth will be of 101m, which is a lot better and in the same order of magnitude than the perceived distance of 100m on the 65" display.

But in these conditions, a point perceived at 1m on the 65" screen will be perceived at 2m on the 40" screen, which is way off and should look quite distorted. And a point that lies on the screen plane on the 65" will be perceived at 1m on the 40". In fact, all the points that would have resulted in an out-of-the-screen effect would be behind the screen plane in this case.

You can try to move the images a little bit more appart to try to obtain better results, at the risk of having a maximal separation superior to the one of your eyes which will cause eyestrain, but the results will be similar as shown in the last column.

In fact, the only way to have the same perceived depth on all displays would be to scale up the image for lower screen sizes depending on the size of the screen the movie was shot for. But you could miss quite a big part of the image then, especially on close-ups. For a movie shot for a 65" display (the biggest size for 3D consumer TVs I know of) you would need to scale the image x1,625 to view it with the same perceived depth on a 40" screen and at the same viewing distance, which would not be the optimal distance to view a movie on this screen size.

¹ Viewing Distance Calculator