Hi Ken,
Yes, StarAlignment can, within certain limits, register images with differing scales. Just try it. If you know that your images have different scales, disabling the Use scale differences option (Star Matching section) can save you a lot of time.
In cases where StarAlignment is unable to register the images (either because they are affected by strong varying distortions, or because the scale differences lead to very different sets of stars), the DynamicAlignment tool is your best option, as Harry has pointed out.