You turn an IntelliChlor cell off by setting it to 0% so CELL light is off.
I have a 35,000 gallon pool and add salt to the deep end well away from the skimmers. If I am adding a bag or two of salt I don't lower the %. If I am adding 10+ bags at the beginning of the season I have the cell off since the salt level is too low to generate anyway.
That caution is there to keep you from spiking the salt level very high which can happen if the skimmer takes in a slug of high salinity water while the salt is dissolving. SWG cells volts and amps are proportional to the salinity and high salt level can cause the cell to get higher power then normal and damage it or blow fuses or burn boards or components.
You need to be more cautious if you have a 5,000 gallon pool that is 5' deep and add chemicals close to the skimmer then adding to a 40,000 gallon pool in the 9 foot deep area.
Pentair makes the broad statement about balancing chemicals rather then just salt because manufactuers hide salt in various mixes under fancy names - Bioguard Mineral Springs being one.
TL,DR - If you know what you are doing you can ignore that Pentair warning. If you are unsure about what you are adding to the pool then setting the % to 0 can protect the cell from possible damage.