There are two issues with the matrix visual when used with multiple rows or hierarchy.
1. color coding not consistent for multiple rows
When I have two rows, few columns, one measure as values and a measure with the background colors for the value (added through the conditional formatting). For all first rows, I can see the background color but when a first row is expanded, all the first rows lose their color. And if I expand any other first row without collapsing the first row of previously expanded one, I won't see any colors for other first and second rows.
2. one tooltip for multiple rows
When there are two rows and only one option for the tooltip, it's confusing on what the hover is telling us. For example, if I have a date tooltip/hover on the second row, it takes a maximum/latest of the dates in second-row items to display as hover on the first row which doesn't make sense. It will be helpful to have an "n" number of tooltip options for the "n" number of rows. Also, it will be helpful to have a toggle option to disable/enable row headers default hovers.