I managed to find a solution to the incompatibility between Point Lookout Reborn and In the Shadow of the Swamp in regards to the Punga Fruit script. Turns out that by deleting (or overriding) the Activator records xx004269 and xx00426a to restore the default Punga Fruit script (xx004e2e) which is modified by ISS will fix the problem (xx = Point Lookout DLC esm).
As far as I know, the Point Lookout Reborn script is very similar to the vanilla script just with its own edits that allow the plant to regrow, something done with the Unofficial Patch. The edits In the Shadow of the Swamp makes are to give the player a random Punga Fruit which are essential to the quest. It was something that was apparently missed with The Wasteland Patch Collection.
Also, the Point Lookout Reborn script (xx0045c8) script didn't appear to work anyway, since I got no message that I received a Punga Fruit.