I think that, really, the key point here is how is that @subpackage information showed by phpdocumentor and friends.
If it produces some sort of navigable grouping, so only (a few) @packages are showed initially and later you see the @subpackages, then I prefer Petr's alternative (we only have to agree about the top-level packages to use). That's better than showing hundreds of packages IMO (David's alternative).
If the @subpackages aren't grouped by phpdocumentor in order to provide easier navigation... then really it doesn't matter too much.
In fact it's a pity not being able to use dots to provide "paths" like "mod.forum.backup" as @package, with each part of the path being "clickable" to the corresponding part of the documentation (much like Javadoc, I think).
Finally, note that I don't buy the final example from Petr at all:
nor David's alternative either, obviously:
IMO workshopform cannot be a top level package in any case. It should be something like:
(In Petr's way)
(In David's way)
But we must keep the root levels well defined for easier navigation and grouping.
That's all... ciao