So in simple terms it's dealing with the employee's position in respect of liabilities incurred to third parties in the course of employment, rather than damage caused directly to the employer through doing the job, Which I think was the OP's concern.
e.g. contrast lowering the flaps too early and injuring passengers, versus lowering the flaps too early and damaging the aircraft.
I agree it's odd that 'negligence' is excluded from the indemnity provision. Then again the whole concept of an 'indemnity' provision at 30.2 seems odd, and fairly meaningless, given that any injured third parties would presumably sue the employer directly for the employee's acts rather than making a knock for knock claim against the employee.
I wouldn't be too worried about it. As noted previously you generally owe contractual duties to your employer and if you breach these duties there is nothing in principle to stop them pusuing you for losses stemming from the breach. There are practical reasons they are unlikely to do this, however, as outlined in my previous post.