The employer takes a deduction for an employer contribution, making it pre-tax. (If the employer fails to take the deduction, that's simply a mistake on the employer's tax return. Such a mistake does not make it after-tax.) Employer contributions such as profit-sharing contributions are compensation to the employee on which the employee has not yet paid taxes.
As I said, employers are not permitted to make after-tax contributions. Employer contributions that are not deductible are subject to penalty.
The taxable amount on the Form 1099-R provided by Vanguard is correct.
Mega-backdoor Roths involve after-tax employee contributions from compensation paid to the employee, not employer contributions.
