Mannequin is designed to be an optional component in CRYENGINE. If you wish you can use 'raw' CryAnimation features instead. Why would you do this? As with every higher level system there are limitations that might get in your way, or might not do what you need.
For simple cases, Mannequin can be overkill. It does introduce some setup overhead.
On the plus side, the system introduces little run-time performance overhead. And using only one system for all your characters simplifies your code, your workflow, and makes it easier to add or remove complexity later.
Note that specifically for non-interactive animation there are good alternatives:
Mannequin is a general sequencing system, so yes you certainly can.
If you use Mannequin as a general sequencer you minimize the number of pathways driving other systems, which makes it easier to do things like network synchronization, debugging, etc.
But: