I know TS already explained, but it's base percentages, this game has three "Base damages", based on the three cores, might, cunning and wit, corresponding to physical, alchemy and esper skills.
It's also a way they represented damage scaling in their older games like MG1K (Monster Girl 1,000), your "base" damage is constantly scaling and changing with the corresponding stat. In MG1K they primarily just used it as shorthand for how multi-hit attacks/skills did damage, so stuff like "40% x3" is 40% of base damage, dealt 3 times with that skill, which technically makes that skill deal 120% of base damage, scaling with the corresponding stat.
In this case, a cause for confusion might be the fact, unlike previous systems, where they typically just implemented magic and physical damage scaling, we have 3 independent scales for 3 different types of base damage, so for example, if there were two skills that each dealt 50% of base damage, if their corresponding skills are equal, they'd deal the exact same damage, however if we take one and made it hit 2 times instead of 1, even though it's still 50% base, it's twice as strong now because it hits twice, plus it'd be more flexible for working both groups and single targets.
However if you have a very low might stat, and a very high wit stat, it doesn't matter if Prime Cut has 100% base damage and Wind Blast across both it's shots ALSO has 100% base damage, because if your wit is more than your might, Wind Blast will do more outright since you've invested more into wit than Might, and those determine the actual numbers.
I will admit, even I kind of forgot about the scaling a few times, since I'm used to MG1K where things are fairly straight forward, either flat numbers and percentages, or only one scaling stat for damage that matters based on if you're speccing a magic or a physical build.
But it's not really complicated, it's just different from other ways of showing damage you might see more often in games, a lot DO just tell you "This attack will do 'X amount' of damage", and others are more vague "This attack does a massive amount of damage".