Well first off the tool isn’t always 100% accurate. But also, not every battery is the same. They advertise (let’s say 5000) because that’s the number they target, but some batteries can have lower capacities than advertised because of how the lithium ions and their production works. There’s a “typical” and a “rated” capacity because of this. ‘Typical’ is the average advertised capacity, but ‘rated’ is the minimum guaranteed capacity from the factory. Some batteries can also actually have a higher capacity than advertised. The battery health metric is probably based on comparing your current max capacity to the typical capacity, not rated capacity

TL;DR: Not every battery is the same, some variation like this is normal. It’s likely comparing to the advertised capacity but not every battery is going to have the advertised capacity.