Hi everybody, OP here. I have managed to achieve resolution to the problem with Apple. By escalating the issue up the customer support chain, Apple has agreed to fix the stripped screws and will provide me a reasonable store credit for the trouble I've gone through.
I'm still disappointed in Apple's repair center for losing my drive. As for their customer support, however, I suppose Danny was a bad apple spoiling the whole bunch.
Next time I send in a machine for repair, I'll likely save a PDF of the system profiler readout, and I might just swap back in the original HD to make sure that I don't risk theft of my data.
Thanks for all your comments, and may you never have to go through this kind of melee, yourself.
best,
Jacob