Your black glass ale bottle is not quite as old as you suggest. It may be a 3-piece mold, if so it places its age in the middle of the 19th century. The double collar lip also suggests a later date. It is less common to see these with open pontil marks such as this one....it may suggest American made.
The bottle has heavy etching from living underwater for quite some time, likely in the ocean. That etching or staining is the result of some portion of the glass leaching out so it is not going to wash away. Accept it as it is.
Thanks for posting all the photos - I removed the zip file and added what I thought were the two most detail-revealing pictures