It's generally understood that the person who writes a will should be aware of the Islamic laws of bequeathing. The writing down is mainly of assets to people/charities etc those who survive you will be unaware of or careless about.
For example you have left your estates and cash etc accordingly but you wish to leave your watch for your best friend. This should be written down.Or perhaps your debtors who no one is aware of. These should be written down because if not once you are no more your property will be then be divided according to the shariah law, and anyone outside of it may not benefit from it.
And yes, a will can compromise the protocol in certain cases, depending on how valuable be the property,your inheritors,etc. However note that any unfairness on the part of the bequeather can then be a sin upon him/her.