Question about updating PHP version

Hello,

A system administrator was working on my server today after someone apearently hacked into WHM (not sure how they did that because i use authenticator) but the managed to create a website and change my root password.

He saw and told me that cpanel is using an extremly inefficient php variant.. something he said like the i varient. Most likely because it was easy to use with multiphp. Is this true and can it be improved to a more effective variant?

And while i am submitting here, how can someone got trough my authenticator to be able to do that? or can he do everything from shell?

Thanks