Geospatial is pervasively Lon/Lat and has been the standard for decades across virtually every software system. GeoJSON is in the correct order, same order as every other common industry format for geospatial. There are similar conventions for polygon winding order, whether a polygon is closed or not, etc which new users frequently ignore.
To someone that works with geospatial data, this is like asserting that RGB is the wrong order for specifying color, ignoring that approximately everyone in industry has been using this ordering convention for a very long time.
It is usually not the end applications that get it backwards, it's usually a library somewhere in the toolchain that bites you where the author wrote code before learning there are conventions for these things.