I cannot replicate your statement "if you make a change outside of the folder
you will still be notified". I uploaded a document in the document library, not
in the folder and I still do not get a notification.
Under Site Settings/My alerts on this site, there is a difference if you setup
an alert for a document library or if you setup an alert for a folder. They are
not one of the same.
Lets say I have a document library called DOCLIB1 and a folder within this
document library called TEST1.
For a document library, it displays: DOCLIB1
For a folder within this document library, it displays: DOCLIB1:TEST1
These two alerts are not the same.
This is the way I understood alerts: You can setup alerts at the file level, the
folder level and at the document library level.