LOAD DATA keeps CPU usage high after it finishes
As expected.

The updating of secondary indexes (INDEXes other than PRIMARY KEY) happens later.  Such changes are stored in the Change Buffer; they are actually written to disk later in a more efficient way than trying to do them as the rows are being inserted.  You will see both CPU and I/O activity.

The net effect should be that your LOADs and SELECTs will complete faster (elapsed time) than without the Change Buffer.