I don't think OSM carto cares about layers unless it's roads. I think it has internal layers by which drawing order is determined and if they are on the same layer, smaller things are drawn on top of bigger. Seems that it's not the case here.

You could use multipolygon to carve out that flowerbed from the pedestrian area. 
1) Make a multipolygon for pedestrian area, with outer role
2) Move pedestrian area tags to multipolygon
3) add flowerbed as inner part of the multipolygon

https://wiki.openstreetmap.org/wiki/Relation:multipolygon

This will make a hole in the pedestrian area, flower bed will be seen through it.

