Quote: But when I examine the actual chip using "Tools-Device Programmig" the fuses are not always set as per the Boards file.
If you look at the full documentation for the Microcontroller on the board, you will get all the information about fuses and each of the bits. You will also get it from the fuse calculator. Hum, I think you already know

.
Regarding Arduino, the fuses are programmed when the bootloader is uploaded to the board.
Sometimes, not all bits of a byte are used - the most significant bits are the one not used. When it's the case, these bits may be set to 1 or 0 with no difference. What I have seen is that the board definition file sets these unused bit to 0, but when avrdude reads back them for verification - during bootloader upload, these bits return 1. And then you get a verify error

... that is false.
If you have a hardware programmer, then you can update fuses settings with "Tools-Device Programming". I can't tell if fuses can be changed in code.
Beware though: changing fuse settings can
brick an MCU. The only way to bring it back to life is to use a High Voltage programmer, and as far as I understand, the MCU can't be on a board.