Following on from the comments above:
The issue with trying to simulate the hierarchy in a geodatabase is that to be in a FeatureDataset all FeatureClass must be in the same coordinate system and spatial extent defined by the FeatureDataset.
Layers in a Group Layer can be in completely different coordinate systems and extents. So if you wanted to group all the same layers in your Group Layer into a single FeatureDataset you would need to project them and ensure they are within the same spatial extent. By spatial extent I mean you could be using a European wide coordinate system but if the FeatureDataset extent has been set to Poland then the UK is not in it (brexit pun! :) )
That could be a lot of work. A possible solution is kind of what you have done, the FeatureClass is prefixed with your Group Layer name, e.g.kn_Blato_1000_. Or you could have 1 geodatabase for 1 grouplayer?
I don't think there are any geo-processing tools that can extract out the grouplayer name from a layer in an mxd, you would need to run this in python. Have a look at the help file for layer object in
arcpy.mapping module to access the property