Well it is inconvenient for the way you want to do things this is sure, However the permissions structure is this.
EDIT USERGROUPS MASTER PERMISSIONS
EDIT CATEGORIES SECONDARY PERMISSIONS.
Therefore given that structure as posted yes if you create a new usergroup you will need to set secondary permissions in edit categories.
So basically your script would need to be modified if you expect it to perform in some other way. We do not support code modifications in any manner. You can try making sure lines 349-398 of adm-cats change to this but if you wish any further assistance you would need to post in THE MOD CORNER which is outside product support since I have not tested this and it is not supported by us.
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