As no response from yesterday, try to investigate more, I found a solution.
So happy day with my 18.04 Mate Desktop upgrade.
Create file and add following lines solve those two main issues.
~/.config/gtk-3.0/gtk.css
.mate-panel-menu-bar menuitem {
padding: 0 0px;
}
Suggestion form “zezic” on https://github.com/mate-desktop/mate-indicator-applet/issues/19 witch I customize according for my need, to 0 and 0 px.