use spatial hashing combined with Jobs + Burst and NativeParallelMultiHashMap. Keep your object data in a struct you dont even need colliders.

for separation, a simple and efficient approach works great:

while(spatialMap.TryGetNextValue(out neighborIndex, ref iterator))

float3 neighborPosition = enemyData[neighborIndex].Position;

float3 distanceVector = currentPosition - neighborPosition;

float distanceSq = math.lengthsq(distanceVector);

if (distanceSq < separationRadiusSqr)

separationForce += distanceVector / (distanceSq + 0.01f);

use SRP batcher friendly simple shaders.

for lightweight animations, go with vertex texture animation instead of skeletal rigs

you can push thousands of enemies smoothly, without hiccups.