CI 3 using native sessions instead of driver

You will probably have the same locking issues with the native session extension. You probably need to spend some time figuring out where to use session_write_close() and to adjust the database to handle more connections and release them faster.

Persistent connections will not help.

Give serious consideration to using file-based sessions.

phpredis extension has much finer grain control with locking; so it should perform just as good as mysql GET_LOCK without database load. You can do the following. (microseconds instead of 1 second).

; Should the locking be enabled? Defaults to: 0.
redis.session.locking_enabled = 1
; How long should the lock live (in seconds)? Defaults to: value of max_execution_time.
redis.session.lock_expire = 60
; How long to wait between attempts to acquire lock, in microseconds (µs)?. Defaults to: 2000
redis.session.lock_wait_time = 50000
; Maximum number of times to retry (-1 means infinite). Defaults to: 10
redis.session.lock_retries = 10

My main question though is if I implemented native sessions correctly? Also I cannot use file based sessions as the application is behind a load balancer on multiple web servers.