Well, 68030s don't run hot, and it does seem that some of the 030 machines were deliberately underclocked so as not to compete with the higher end models, like the IIsi over against the IIci, the processor in the IIsi being perfectly capable of running at IIci speeds, even though the model was clocked slower.
Use of the chip with those markings in the faster machine could have been just a cost-saving measure, after there was a batch of 68030s produced that proved to be better than expected or some such, or maybe the factory simply put the wrong stamp on the chip.
It is a little odd, however, that we two have discovered the same thing simultaneously in two different 25MHz machines of the period. (Interestingly, the LC520 is spoken of as architecturally very similar to the LCIII, much like the LC475 and 575, so maybe it occurs in these two models only.) Googling turns up nothing on it for me beyond this thread.
I can say that the board with the chip marked 16MHz has the same components as the other LC520 board currently in my possession, but some components have been moved around very slightly. So presumably it is an early or late revision that I have.
I'll try to take some pics for the Flickr group before I sell the boards.