First off, I think you've made a good choice in choosing a replacement for your Miatas. From a driving enjoyment standpoint, you'll never want FWD again.
Anyhow, I don't know as much about the convertibles as I do the sedans and coupes, so I can't answer your questions about the back window. As for options/packages, if your Mazda is anything like the most of the Japanese makes, it pretty much comes with all the options standard. On the BMW, it's going to be hit and miss on options/packages when you buy used.
Depends on whats important to you, but here's some of the packages/options you'll see for the current 3 series -
Sport Package -
Sport suspension
17 inch wheels
sport steering wheel
12 way power sport seats
Premium Package -
Myrtle wood trim
8 way adjustable power seats
Power moonroof
BMW OBC (on board computer)
a few other items....
Xenon Headlights
Harmon Kardon Sound System
Heated Front Seats
Navigation System
etc. etc. etc.
To answer your question on the designation - I've seen them noted as a 323CI convertible or 323CIC - not sure which one is correct

used (it's not a 323ic - the 'ic' designation was used on the previous generation 3 series - the E36)
Good Luck