The program accepts that you put any berry, whether you have them in your Chest, or not. But if you don't have that berry, some Pokemon won't get on the list, because the mini-game requiring berries won't get "played." That's all. The guides use Oran Berry (#7), because it's the most common one, and it's useless to high-level Pokemon.
Lugia is back online, the forums are just not using the same URLs as before. This is what the Original Post says:
Source: http://www.lugia.co.uk/forum/index.php?topic=7419.0