I have the 669GL 5 wire, but I don't have any flickering issues using VGA. Is this installed in your car already, or is it on a test bed?
It should be possible to resize the desktop when using HDMI. Look at the Intel graphics app in the task bar and see if you have some sort of scaling setting. I have a micro ATX motherboard that I use for my HTPC that uses the onboard Intel graphics, and there's a way to scale the desktop by percentages - I don't have it running right now so I don't remember exactly where it is in the config app. Sorry.
I have had zero luck doing any kind of DTD modifications with an Intel graphics chip and this monitor.