Yup. If you wanted to match the tabletop as closely as possible, the repeater crossbow would have a higher AP damage than a regular bow, but lower non-AP damage.

But, remember, the table-top was constrained to a very, very small range of Strength and Toughness. Like, 95% of the units in game had a strength of 3-6. IIRC, literally the only units in the entire game that exceeded S6 were war machines, characters, a small number of monsters (eg, the Star Dragon was S7, every other Dragon had S6), and Black Orcs and Blood Knight on the first round of combat. The only units in the entire game with a strength of 2 that I can think of were Knoblars.

So, you have almost everything's strength, from a Giant down to a goblin, broken down into only 4 levels.

Most of these special rules are just in place because they needed a way to try to make something distinct. So they wanted to make Repeater Crossbows hit a little harder than a regular bow (S3), but not as hard as a regular crossbow (S4). There's no S3.5, so they gave is S3-AP. Want a Dark Elf to hit a little harder than a human, but not as hard as a Saurus? Murderous Prowess special rule.

Because Total War isn't constrained to just S3 to S6, these special rules aren't necessary. If an Empire swordsmen in 22/6, and DE swordsmen could be 25/6.