For a web-based SaaS, I could see them doing something like "Web-only access including mobile web, $10/mo" and "Web + native mobile/API access: $15/mo" -- then only offer the latter option in-app.
I suppose you could try to classify Android and iOS API access differently, but I suspect that might be a little over the line in terms of trying to slip it through the app store review process.
I do still wonder how third party apps to hit a subscription API are going to work, though. I suppose a lot of those will be for-pay so Apple gets their vig from that anyway, but it's always possible someone will decide to release a free one...
This would work for apps where the mobile UI is only an adjunct for doing real work on the desktop version.
All of my apps are planned to be free, ad-supported, with in-app purchases.