I think I have found an interim solution, however, HP you MUST FIX THIS! This is a terrible way of having to set it up and it definiterly does not encourage me to buy HP products in the future. Please fix this and push a Mac driver update or printer firmware update or whatever is required.
Here is what I had to do but I am not confident that it is going to actually work all of the time :/
The different applications seem to have different key names for each of the individual settings in a printing preset. So a preset made in Safari would not work properly in MS Office. However, if you create a preset in Word it sort of works in Safari. In Word's print dialog, I first set the paper size to scale to "A4 Two sided margins", then selected the two sided print option and saved this as a preset. Here's the weird part; the two-sided checkbox is ticked if I select the preset but if I go into the "show Presets" option that shows the details of the presets, it says that two-sided printing is off! The same weird thing happens in Safari's print dialog. It is because of this contradiction that I don't really trust this solution but it seems to work for now.
HP FIX THIS PLEASE!