The problem doesn’t really have anything to do with that cloner specifically or even EM mode vs HID mode. Definitely check out this thread: https://forum.dangerousthings.com/t/quirks-of-the-t5577-cloning-tags-to-the-xem
In short, the cloner can read HID ProxCard II cards and EM41xx cards, then set the ATA5577 analog settings to the appropriate configuration to emulate the desired card type, then write the ID into memory.
If you don’t have a good coupling during this write process, the ATA5577 can “tear” and you may end up with a bricked tag. Definitely read the thread.