Probably way off beam .. but I was told this many years ago ...
Years back on single track railways they carried a "flag" which was permission to move along the track, without the flag you could not proceed onto the next section - this was to avoid a head-on collision. At the end of each single track section was a short piece of dual track where the opposing engine would wait, or if there was no opposing engine, there was a receptacle for the flag. There were often fuel/water facilities at hese ponts as well.
The origin of the phrase "flag stop" came from this short stop over to collect the flag and/or resupply.
Proabably an "urban myth" but I don't think they existed when I was told this !!