My take:
1. Magnepan should have communicated with you promptly once they received the damaged speakers and should not have waited five weeks to give you an estimate. I assume you now have the estimate and the insurance claim is in process, right?
2. Shipping crates- cost more money than cardboard and styrofoam to fabricate, and add to shipping weight. If they have experienced alot of damage by cheaping out on packing, it would be self-defeating, and more costly to them in the long run. But, is it clear that your seller used the original shipping cartons and packed them properly?
3. Turnaround time- you should have probably been told what to expect when you first contacted Magnepan. I don't fault small companies for this- it sort of comes with the territory. When my Lamm L2 started acting up, I called Vlad and was told they were leaving for the Munich show and wouldn't be back for a month. He's a one man band. Had to wait until he returned and then drove the units to his house/factory because I'm in NY. He repaired it quickly after that, and the initial wait was frustrating, but I adjusted my expectations, and bought something to use temporarily in the interim (which I thereafter resold once the Lamm was repaired).
4. This is one of the downsides of buying stuff used or from private sellers. I'm not advocating buying new from a dealer (I have taken advantage of used equipment here and through dealers), but the premium you pay a dealer should cover delivery and set-up, loaners when there are issues and generally make your life easier. They may also have more clout than you, as an end-user. The dealer I rely on locally makes house calls, delivers stuff, provides loaners, takes trade-ins and is responsive to emails and phone calls when i have questions or needs. That's why I go to him. I don't think about the premium there because at the end of the day, it's worth it.