I'd like to note that "crop rectangles" here refer to the region of the virtual image canvas, whose size is recorded in the image header, where each frame gets

I'd like to note that "crop rectangles" here refer to the region of the virtual image canvas, whose size is recorded in the image header, where each frame gets decoded. So here what's being cropped is an image canvas, not a frame. Your point still stands in the sense that, if those rectangles exceed the canvas extent, the surplus will be indeed discarded. I believe the current libjxl doesn't produce such image anyway (why do you keep a portion of image to be discarded?) but it is still something to note.