Hallo!
The first one found would be the right one. It's not pd's problem if there exist more than one file with the same name. Surely that's up to the creators of the files to sort out.
Well, this is now discussed since years. The whole namespace+pd-extended thing would not be obsolete if we simply would load everything in the extra directory ...
Also every external in there would be loaded into the memory when you start pd.
LG Georg