The problem with the "Spells" entry in the MM Glossary (which is where the bit in the SRD appears to come from), is that it pretty much says "Check out the PHB for how this works." And the PHB says nothing sensible about everything being either Ex/Su/Sp/Na/w/e.

In the organization in the Monster Manual, it seemed totally unclear that "Spells" is actually a special ability, though the SRD organization seems to make this clear. I guess we can figure it out from the definitions given for Special Attacks and such, but I find this kind of connect-the-dots RAW to be poorly conceived at best.

But generally I agree that just because we can determine x or y about "Spells" in the MM doesn't mean we can determine that the "Spells" in PHB works the same way, nor that the systems set up in the MM and later versions of it are retroactively applicable to the class features in the PHB.

Moreover, if they felt strongly that it was an oversight, then they could have errata'd it. They didn't, so I'm left feeling that they thought the PHB's class features were fine as printed.