You can use the xfeditdb utility to rename databases before merging them. When you merge the databases, the single feature combines the usage of both applications, which can be plotted with xfcustomreport.
The command syntax is as follows:
xfeditdb -renamefeature database.db old_feature_name new_feature_name
For example, say you want to combine my_feature_A and my_feature_B. You can rename both features to my_feature_AB:
xfeditdb -renamefeature database.db my_feature_A my_feature_AB
xfeditdb -renamefeature database.db my_feature_B my_feature_AB