LyX assumes that a standard paragraph following an aligned one or
a layout with NextNoIndent==false has to be indented on screen.
This means that in the latex output a blank line has to follow.
In this case there should be no problem as regards extra vertical
space and it simpler and more elegant to simply uncheck "Indent
Paragraph" in the Paragraph settings pane rather than changing
the current logic and allowing to insert a parbreak separator.