If I am short of 5 gallons at bottling or when I transfer to secondary can I add spring or purified water at this time?
You can always add water to make up the volume. Just be sure the water is sanitized, like boiled and cooled. Boiling is best because it also removes air/oxygen from the water too which slows the staling of the beer.
However, adding water will dilute the current flavor, aroma and bitterness profile. If you are OK with that in order to get a full 5 gallons so be it. To me its not worth it. Just bottle what you have and be more careful about volumes on the next batch.