waren, the OPS 1 (Jar or EU) requires 5% only, allowing to reduce it to 3% naming an ERA, or by using DDP (decision point procedure) or some other procedures I personally find quite complicated (the DDP is another one indeed, in the past it was much simpler).
What they should include, in my opinion when calculating the second sector fuel, is a sort of manouvering fuel to cover apu running during transit time.