Some more info that may help in adapting the code in the plugin:
This the part of the code that extracts each individual tiddler from the incoming data and then saves it: https://github.com/saqimtiaz/tw5-plugins-sandbox/blob/e9ebad0708d6c15eb0b8974a3d9328e3b0c0e9af/plugins/sq/ExternalContent/load-wiki-actions.tid#L20-L35
It is the usage of $action-setmultiplefields here that led to the inadvertent merging of local and remote fields, for an overwrite it should be preceded here by deleting the local tiddler for an overwrite. Note also that rather than manipulating the $action-setmultiplefields in that code which can get hairy, it can also be followed up with $action-setfield to further add/manipulate fields