The structures of a base (launchpad, runway, taxiways, buildings) will flicker when viewed from above 5000m if the field around has a light color (for example DSC has a field arround it with a dark green color) or if the elevation of the base is under 3 meters (2-3 meters is pretty high)
Found a way around this bug.
When placing a base, having the flattening disabled, find a place where that base is fully surfaced (doesn't have patches of land covering it). After the base is placed in an area where it's fully visible you can enable the base flattening to even out the soil.
If you place a base in an area where it's partially covered with patches of soil, even though you make spots of soil disappear by enabling the flattening, once you go above 5000 m the base will flicker.
In other words terrain flattening doesn't do the job fully once you are more then 5000 m away from it.