For cal courses that are an even number of tape lengths, this is a moot point. If you put down a second set of duct tapes they are going to be in the same place as the first set, and there is no reason to do that. Since many people do 300m or 1000ft cal courses, that statement in the manual could be confusing.
For courses that include a partial tape length, using 2 sets of duct tapes has the advantage of being closer to a "blind-blind" process, i.e., you don't get to see how the comparison is going DURING the second measurement, only at the end. But that's a small thing that may not be worth dealing with all the extra pieces of tape. I use a 100m tape, so a second set means only 3 extra pieces of tape. No big deal. For someone with a 100ft tape it's a lot of extra tape pieces.
That statement in the manual is from the original, not something that was added in the last couple versions. No one suggested changing it until now. Maybe in the next version.