The app that I am trying to submit is for a field sales system that is already running on Android devices, and which we are now trying to make available to Apple users. It is a cloud based application, and users synchronize data stored on their devices with data stored on a web server. The application is sold to companies rather than individuals. Each company has many users, all of whom synchronize with the same database on the server.
We maintain our own web server and provide a hosting service, and companies can also host their own servers:
I understand that we are not allowed to mention the Android platform anywhere in our app. I also understand that we have to allow all subscriptions, registrations and upgrades to be paid through in-app purchases. But I have a number of questions:
1) I think that as long as your clients are aware that the iOS flavour of your app/service was limited in some manner (tell them the rest is work in progress) then I cannot foresee any issue with this. You may still consider ringing Apple Developer Support and run it past them, but your chances of getting a non-vague answer from them directly are still high - they'll probably say it depends on the reviewer when you go to submit the app.
2) Sounds fine, and not uncommon in the enterprise app world. See 3) for more details.
3) You can utilise the VPP (Volume Purchase Program) to achieve this, but it's only available in the US at time of writing. See the link below for further information:
http://www.apple.com/business/vpp/
I think that another way you could consider app distribution and which would let you bypass Apple (to a degree) is to sign up for an enterprise developers' account. This will let you build the usual development & distribution builds of your app, but a distribution build can take two forms: limited to devices by their UDID (100 limit still in effect) or not at all. If the latter, you could self-host the generated .ipa app file, which is perfectly viable.
4) Registration keys for the app? (to unlock "premium" content or as the method of app activation?)
Hope this was of some help, best of luck!