As far as I am aware, SoftTH doesn't know, nor can do anything, about screens of different physical sizes.
If the smaller screens are lower resolution, by the precise amount that the screens are smaller by, so that your pixel size ends up the same, then in windowed mode things will appear the same size, although you can't compensate for the bezel gap. SoftTH and LFS can both compensate for bezels (although LFS can only do so when rendering with multiple viewports).
With SoftTH, when you run a smaller resolution on the sidescreens, the whole image is still rendered at 3x the central resolution, and the image for the sidescreens is resampled to the lower resolution. If the screens are smaller and the native resolution lower, what would actually be better is for the image to be cropped, rather than resampled, and that would probably get your desired effects. I've not noticed an option to do that last time I looked through the SoftTH config, but there might be. If not, you could always add a request for that feature on the SoftTH forum.