Perhaps the designers were simply sure to include the +1 CL/level for classes that were not designed as pure casters and the +1 CL/level was just assumed for pure casters.
What do I mean: for Arcane Trickster, Eldritch Knight, etc. (your 2E multiclasses - rogue/mage, fighter/mage, respectively), it was necessary to include the +1 CL/level because it would not be immediately obvious that that was or should be the case.
On the other hand, pure caster PrC's are merely an extension (a focused externsion, at least theoretically) of the original, so the +1 CL/level is just assumed.
I am not trying to say that any of this is obvious or that it shouldn't have all been written, but to me it makes sense and is simple to intuit.