If a photo is imported from Photos, it would be good if you had the Save over the original photo option where you are prompted to allow the app to modify the photo. This is a feature that Pixelmator has and is a real time saver if your intention was to replace the original image in the first place when working on a number of images.
it is also not permanent in the sense that if you go into the modified photo in Photos, you can tap on the edit button then tap revert to switch back to the original photo instead of the modified version.