What about methods, typically called "package" or "protected", which are not part of the public API, but must be called by other classes that are part of the distro? Those should not have leading underscores, IMO, because it contradicts standard practice. From perlstyle:

You can use a leading underscore to indicate 
that a variable or function should not be used 
outside the package that defined it.
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The Pod::Coverage problem is solvable with minimal effort, as both you and xdg have pointed out (thanks). However, there is still the need to document these methods while indicating clearly that they are not available to users.

There seems to be a range of opinion on as to the best solution. The ones that I like best for this project at least are the ones closest to javadoc, but I can appreciate the merits of the document-by-test and the bury-private-docs-deeply schools as well.