Experienced similar issues with a 20x annual spend on Apple gear. After a laundry list of issues with Apple Business and some repairs we switched to buyint from a procurement partner (CDW) and moved device repairs in-house via Apple Self Service so that we aren't stuck with overpriced flat-rate depot repairs.
Like the iPhone Upgrade Program, it's probably best for businesses to lease devices from Apple than to deal with all the nonsense around repairs.