Bring it on. The Mail Archive gets tens of thousands of inbound messages daily, and currently serves on the order of queries per second. So I don't think there is any concern about swamping the service given the numbers mentioned. Doesn't matter to use how many mbox files are involved for imports.
You are pretty much right about control; we ask list admins to be the primary contact with M-A staff and they may request deletion of a message or their entire archive at any time. As far as the logos go, uploads are reviewed by M-A staff before going live to prevent "logo spam". So far that has been a sufficient level of review and I'm not aware of any logo problems - at least nobody has complained so far. Language localization is handled the same way, and that's pretty much the extent of archive customization. Finally, no problem if you want to create your own index. Thanks for asking and we hope to, um, win your business. Cheers, Jeff