In most cases, the Boot Down Preferences can be left alone. Changing the preferences is only necessary in a few special cases.

Avoid boot block writes

If set (default), attempts to write to the boot block area (0x0000 to 0x0800) are simply discarded. If you uncheck this box, then it is possible to write to the boot block. Writing to the boot block is very likely to destroy the bootloader. Also note that you can set the config bits to protect the boot block.

Vendor ID

If you are using a modified bootloader, you can change the USB vendor ID. The default Microchip vendor ID is 0x04D8

Product ID

If you are using a modified bootloader, you can change the USB product ID. The default Microchip bootloader product ID is 0x000B