Harmonizer: chord suggestions made from User scale?

Yes.

Make a palette based on that scale and save it as a new Scale Set to the Catalog.  It will then appear in the menu for selecting the "Key" for the Harmonizer.

Just tested this, but trying to save a palette as a scale set (Export >> Save scale set to catalog) gives me a runtime error. Crash report submitted.

Thanks for the crash report. This affects the standalone Palette app only. It works from the Palette tab in the arrange window.

For an alternative Scale Set to appear in the menu, the Harmonizer's input must at least partially match it. The menu is populated with suggestions matching the input, not with a complete list of all keys:

Sorry, yes. It needs to be enabled in the scale selection preferences (Edit menu, or progression editor). 

However, there' s a bug that currently prevents this setting from being updated. Therefore it needs to be set from the very beginning, after opening an arrangement, before opening the Harmonizer tab. 

A fix for this will be included with the next build.