Presentation of the data is the issue here, not calculation.
First, I don’t think that modifying CTL/ATL is the way to go. These are established metrics for total training effort, though they do suffer from the problem of relying on the imperfect metric that is TSS [which assumes that an interval of 350 watts after 10 minutes riding is the same as an interval of 350 watts after 3 hours of riding].
Second, stacked bar charts are seriously difficult to read. I could have my fitness chart showing long periods, such as one or two years, meaning that there are 52 or 104 such bar charts to compare. The alternative to stacked bar charts is grouped bar charts. like you have for the weekly time in zones. But 52 or 104 of them would be information overload!
But the advantage of this line of presentation is that the charts would be separate from the current CTL/ATL graph. At the moment, that is an elegant representation of the data, not to be carelessly thrown away. So I conclude that the most appropriate option for such data would be a separate chart of CIL/AIL that parallels the current CTL/ATL chart. This could be either an option offered at the top of the existing page or automatically populating the existing page.