The reason for that is the Havok node "BSIsActiveModifier" which is used to set and control Animation Variables. This is extra functionality, and takes 2 units (when the "-md" parameter is NOT present).
If you use the new AGO patch in FNIS for example, the number of possible animations will automatically drop, although AGO doesn't add custom animations (only animation replacers and a few behavioral changes). It is dependent on certain types of functionality in the behavior files.
FNIS XXL will also calculate the contribution of each FNIS depending mod towards this limit. Starting with V7.5, FNIS will warn you when you have reached the critical animation limit. Everything else has its penalties, and that can bring down the limit to 9,000 and less. Of course only the most simple we know: basic animations, as they are used in poser mods.
For both LE and SE we can install up to 26,162 additional animations. Skyrim has a hard limit for custom character animations.