Include an option where window transparency doesn't fade out the contents of inactive windows.
Though visibility is always going to be maximized by disabling transparent windows, this change would still greatly improve visibility for those who choose to use the feature, as demonstrated in this example:

I feel that the feature is underutilised but has great potential if we could refine it a little bit. Improving visibility of inactive window elements would be a relatively simple change, and the feature would get more use. Bellow is an alternate option, less aggressive in fading window contents:

Including additional options such as 'permanent transparency' along with 'use alternate color for active window' would give user better control over their ui aesthetics, maximizing visibility of their project, allowing them to more easily see relevant information contained within transparent windows.