The Photo Resize app makes your images square by adding white space to the shorter side of your images. This means that it's limited to the original size of your images. If the original images are not the same size, the resized images will not be the same size. As a result, the products will not necessarily look aligned or the same size on your site.
However, we have another app that will be able to achieve what you're after for only $0.25 per image - the Retail Ready Photos app. You can submit your images to us and we can resize them and apply a template so that the images are all the same size and the products occupy the same space in the images, which will align them on the site. Go ahead and give it a go - you will get 5 free images when you install the app.