You are not the first person to mention the difference in wear. I sent photos to professor at Princeton he was very sceptical that it genuine signature, believing that it would have been added perhaps several hundred years later when the wars were over and adding big names to help sell swords was done.
I have reached out to several well known dealers and the consensus is that it is an old Tachi style katana. Dates given have been broad from 1400 up until 1675. This is obviously conjecture as they have not seen it in person. Woody Hall is going to polish a window area to see if it is worth polishing the whole sword. He will check the spots that are showing to see if it can be polished out or if the underlying steal is showing. It has been polished so many times not much of the cutting edge remain, he will also check the tip to make sure it still has not been damaged beyond repair.
All in all as a novice I am most interested in it's age and history and preserving it in the proper way.