There are two Base File configs for OSX. There is the Base File.sublime-settings and Base file (OSX).sublime-settings.
There are only three settings in the OSX file for font and scrolling past the end. I was wondering why these are not in
the Base file.sublime-settings file. It took me a while to figure out that this file was overwriting the scrolling past the
end because you can’t access the OSX file in the preferences menu just in the packages folder.
thanks

The Base File settings are applied in this order:

Default/Base File.sublime-settings
Default/Base File ().sublime-settings

User/Base File.sublime-settings

The platform specific version exists so I can ship the same set of files on all platforms. In general, your best option is to edit User/Base File.sublime-sittings, as the next time a new setting is added, Default/Base File.sublime-settings will be overwritten.