What is the meaning of the caution in hardware manual of a microcontroller
The manual is poorly written, but I think what they are trying to say is that if you do not program the register for a documented alternate function then the behavior will be undefined. For example, I would assume that programming any of the registers for the 3rd, 4th, or 5th alternative would result in unpredictable behavior at pins JP0_0 through JP0_6. Likewise, that the behavior of pin JP0_6 is unpredictable for any of the alternate modes.

However, the OP should provide a link to the original document. There is almost certainly some important context that is missing from the question.