Indeed. ShapeData 'BackgroundColor' gets precedence over a linked shape's alarmcolor. It does however not override the highlight and selection styles.

With what I see in your other shape data it seems difficult, but the only way out currently is to put a regex of sorts on your BackgroundColor that replaces into an empty string when you don't want to display the green default color.

The only other non-scripting I can think out of this is to use a param placeholder to retrieve the right value and then extrapolate towards a color, but I can't tell from your use case if that's an option.

Finally of course, there's the option to execute a script in the background and set a variable from the script that is then used in the BackgroundColor shape data. Dirty solution though and at that point you might want to create a feature suggestion.