Any preview pic from my mod is indicative of the option to disable those flagpoles, as you never see them there. There are two ways to disable them. Either in game, in which case you go to the options for Battle interface and set the "Floating flags" for "Land units" and "Ships" to "Never (show)"; or before game, in which case you go to the preferences file, and set the values for "ui_land_units_ids" and "ui_naval_unit_ids" to "2" (=never show), save, and exit file.
Edit: didn't see that second post of yours where you had already figured it out.