Apparently they were optional?? I don't remember them being presented that way but maybe in a later book or Dragon article this was explained...
"Allowing PCs access to prestige classes is purely optional and always under the purview of the DM" (3.0 DMG, p.27). I have been told by people that they were, originally, presented as the same in 3.5 as well- at least until mid to late 3.5 at which point it went from went from a) Andy Collins, in Dragon, telling DMs that PrCs were an optional tool for word building and, if including them to be selective to b) his Sibling Rivalry article telling DMs that they should find a reason to a include a given PrC if the player wants it.