Even when syncing, user preferences like font size, theme, extensions loaded, window positions, screen layout etc are not copied between machines and are thus independent. When you install Moneydance it has default settings and these are not based on screen resolution.
I have different machines with vastly different screen sizes and resolutions. I have set up a small Netbook to use a completely different sized font (Menu: File --> Preferences on General Tab) and have also set up the summary page different on the device to only have the side bar and one column (Menu: File Preferences on the Summary Page Tab)
So it is necessary to set up the screen preferences for each machine. Different themes may also work better on specific systems.