This is a new concept since Application Server Version 1.54.17340.3 (Release 2017-11-23 Nuthatch MR1).
Previously, when doing a generic custom import, you had to choose the same spatial system as the features you wanted to update had. If the import discovered a feature with a different spatial system than the spatial system in the import, the import created a new feature.
This still holds true if you specify a spatial reference system in the import configuration. However, if you don't specify a spatial reference system in the generic custom import, the import will only look at the feature name when updating feature or observations or creating new observations. Consequently, new features created will not get a spatial reference system.
For more information please read: