The "capacity" is only used for runtime estimation, and especially in the modern era of wildly-varying SSD mods is going to be inaccurate.
The actual "battery level percentage" is based on the battery _voltage_, and for a given battery chemistry, will be fairly accurate with different capacity batteries -- as long as they share the same chemistry (and therefore, discharge curve) as the original iPod battery.
Given the sheer variety of replacement battery options (manufacturer, capacity, quality) the odds are high that there is a wide variety of battery chemistries in use.. so we have no way of knowing what your (or anyone's) battery's discharge curve looks like.
So. If you want a more accurate battery meter for your player, there's a so-called "battery benchmark" plugin that you can run to generate a voltage-over-time data set that can be used to create an updated table. The idea is that you start with a fully charged battery, start something playing (on repeat), and launch the plugin. It will run until the battery dies completely.