Hi and welcome to the guild.
No doubt your fully aware but just in case and for anyone else wandering by then a couple of general, free, open source soluitions to the GIS issues are QGis App and the library of functions for processing GIS data in the form of GDAL (of which QGis uses).
A lot of the software that we use around here are either paint packages or applications which provide a nice result but are in no way scientific or quantitative. Several of the mapping programs that are used have geo-referenced map overlays. One that springs to mind is GlobalMapper. But most of them do not and much of the fantasy mapping is more concerned with the artistic result that the geographical accuracy.
So I think in a nutshell that is the main difference between real world GIS style and fantasy. Real maps also have the ability that someone can measure the map and infer real distances, but in fantasy, since you cant go to the place your mapping, then its not useful to do that so artistic quality is more important than accuracy.
We also sometimes talk about historic maps that are not fantasy and yet also have the property that they have no shape or space relationship with the real land. The very old maps like the mappa mundi etc serve to solve real world problems but do it in a way that is not at all like the way we do it in the modern times. The closest example I can think of to that are the subterranean maps of London's tube system. For the same reason in that you cant go to the space in-between the lines, the map has been heavily warped so that it looks good and makes it easier to put on all of the station stops. The relative real distances between the stations bears no relation to the distances on the map.
So whilst there are some real world examples of why it might be important to show how fantasy mapping can have some modern relevance its no where near as important as the GIS & tools for most commercial real world maps.
It is however, much more fun !
https://www.qgis.org/en/site/
https://gdal.org/