Is combining books with each other first always better?
Not always. Pairing lowers the prior work penalty, but you pay twice for enchantments that appear in the combined books. With few books, adding straight to the item can be cheaper; with many, only pairing keeps steps under 39. The calculator compares both strategies for your set.
What if a step goes over 39 levels?
Switch the criterion in Options to see the lowest-step plan, pair books up, or trim the plan by removing an expensive enchantment. A piece with high prior work is almost always the cause: items used 5 times already carry 31 levels of penalty.
Do the results apply to Bedrock?
No. The rules are Java Edition. On Bedrock, according to minecraft.wiki, the enchantment cost uses only the difference between the final and initial level on the target, so values are lower and the best order may change.