The borderless:true setting is responsible for the borders of the widget itself.
The layout as a container widget has one more property to control the borders of its inner views: the type. By property defaults to "line", which sets 1-px border to inner views (trees and resizer in your case).
in my example, http://webix.com/snippet/58e91298, if didn’t hide the second and the third child view, then everything is normal, but after hide the second and the third child view, the layout show top and bottom border, this is not normal, so layout’s algorithm has a little problem.