Just in case someone cares, I just tested the paged comments plugin and it functions just fine in either plugin directory.
As a note, I wanted it as a global plugin.
It has its own config file, which gets included on each run, but it also declares the same settings (as a default) in the main plugin file before it includes the config file. So, to save an include, I just set the defaults in the main file to what I wanted and commented out the inclusion of the config file.