Ah, I forgot to mention this: PDFCropper can set different settings for odd/even pages. This is because they can have different margins, etc. so you may want to set them separately. However, I don't use this: when I open a PDF, I unselect both the Odd/Even and First Page is Title Page checkboxes. Then the grey area changes all pages.
Crop settings are for making it reflow, I think. There's a "Reflow Frame" option that I tried once before... you set the page size and it reflows the PDF into a PDF of that size.
As for registration, the program is registered to your computer, but if you have a USB hard drive or something like that, it can use the hardware ID of that drive in its registration. This means that if you ever get a different machine, as long as you still have that drive, you can use the program.