Piranha Plant is a special case because it was clearly meant to be part of the base roster as the game's "surprise character", but they didn't have enough time to do so. Hence why for awhile, it was a free bonus.
Mewtwo, Lucas and Roy are also a completely different thing because they're veteran characters that have already had their foot in the door. There's a different standard.
There's no "clearly meant" at all. That's just a guess we have due to data we found a long time ago. The only actual thing we know is it was worked on while the base game was being worked on, which is a reason for the Palutena's Guidance.
Data can be interpreted many ways. It was likely meant to be DLC in the first place. Sakurai figured out the base roster a very long time ago. The way he speaks about it is that plans were kept in stone. It's not beyond clear on that front either. So we really don't know if it was ever meant for base, or if it was always bonus dlc from the start. The only thing we know is that Sakurai chose it at the same time as other base characters, but that's iffy too. Especially with rumors that Banjo was chosen around March 2018(I might be misremembering the Banjo rumor, though. If this is wrong, somebody please say something) This isn't when the character was worked on, but PP could've been chosen as early as August for all we know. The data didn't start existing till as early as September, which gives no real information either.
The data does lead to that as a possibility, though the Guidance means nothing as PP was programmed well before the game was finished. But considering it released really fast after the actual game did, and unique characters take around six months or more, it makes perfect sense to find game data around September 6th. To further clarify, the only thing pointing towards it being base is that the placement of the file was near other base game characters, but not at the very end. Every character was accounted for besides it. However, we don't know if the order of game data has anything to do with the exact "roster placement" or if it was just when they were worked on. Take Jigglypuff for example; usually it's near the end of the game data, but it doesn't mean it was always going to be cut either. Nor DLC. It just meant it was one of the last characters finished. It makes a lot of sense to work on PP late into the game if it was directly meant for DLC, so the data more or less doesn't say all that much.
That said, Sakurai may eventually give us more clear information. It's not like we should've known PP was even in development of when it was(anybody who paid attention to his earlier articles would know it was worked on before the base game released, anyway. Which already, as I noted, accounts for the Palutena's Guidance).