Boot images usually have dedicated purpose and most of them are related to other contents on the disc.
WinISO will try to recognize the boot image type which is widely used by Windows installer discs and Linux installer discs.
For the recognized types, WinISO may modify the boot image to make sure it will work properly.
For the unrecognized types, WinISO will leave it untouched. But any changes of the disc image are likely to lead the boot image not to work properly.
It is not recommended to modify the special purpose boot-able disc images directly by WinISO. If you stick to doing so, you're going to get a boot failure message in most cases.