Godot's physics engine is indeed not deterministic, but it doesn't claim to be. Most games don't need determinism after all :)
Godot is a general-purpose game engine, but it happens that fighting games have specific needs that aren't well-addressed by general-purpose game engines.
There are plans to make the physics engine more deterministic for 4.0, but it will never be 100% deterministic by default since there are too many compromises to make for that to happen. Due to this, if you create a replay system, you should make it store players' transforms instead of players' inputs. This also ensures engine/game updates don't break your replays.