Intel Atom® Processors based on Braswell, Cherry Trail and Bay Trail platforms do not offer support for Custom Scaling. This is because the display hardware is limited to only one display scaler.
In principle, the display scaler could be used for Overscan compensation on HDMI. It could also be used in a game with a swap chain resolution, which is different from the panel native resolution.
Trying to switch the scaler on the fly between different outputs dynamically would be very complex. (For example, how to anticipate which output should get the scaler and for what usage?) For mobile systems with an internal panel, it made sense to bind the scaler to the internal display because that's the panel that is "always there." So it provides clean support for those local usage models, such as gaming at non-native resolution. For a desktop system though, no internal display means the scaler should in principle be free to bond to one of the external outputs.
Newer Platforms based on the Intel Atom® Processors like Apollo Lake and Gemini Lake don't have this single scaler restriction. They have scalers for each display pipe.