If you type "fill" in the Timeline Search Bar and then select only the layers you want to change, you can use the toolbar to change only the selected shapes.
Unfortunately, you cannot add modifiers to the Timeline Search. A good feature request would be to be able to search for fill and color to eliminate the stroke colors from the timeline.
The only other option without scripting would be to open the Essential Graphics workspace, type color into the Timeline Search bar, and then drag all of the Fill/Color properties into the Essential Graphics panel.