I'm trying to move out of ArcGIS into QGIS permanently for basic operations, so be patient please. Here is the problem. I'm trying to georeference a topo map in EPSG:22523 (Corrego Alegre UTM). I did the regular procedure, which has worked before for WGS84 stuff, and is also shown in QGIS tutorials, including this one: http://www.qgistutorials.com/en/docs/georeferencing_basics.html
However the georeferencing just doesn't work. When I open the layer properties in the project, the CRS for the layer is actually WGS84 (4326). In the link above a user asks the same question, and his conclusion, after not getting an explanation, is that setting the layer CRS in georeferencer correctly is just useless. You still have to put that CRS in target SRS in transformation settings. However there isn't a single georeferencing tutorial where this is mentioned. In fact they all put target SRS different from layer CRS. Please help.