Yeah I still don't understand why the Khan Academy and other educational/open source developers are using Google App Engine when it suffers from vendor lock-in.
some of it yes, but if you write modular code then its a none issue. Doing Java development, GAE supports most Java EE and popular frameworks, so if done correctly porting would not be an issue. I can't say the same about Python stack.
Unless you're doing regular integration testing on an alternative platform, you're bound to inadvertently introduce some painful GAE-specific dependencies.
It's still an issue -- you have all this data that you have to migrate off of app engine. Some of my friends who migrated on to GAE said it took them almost 2 full weeks to load data into GAE, and now I'm sure it would cost them at least a full month to load data off GAE. The code changes are probably the easy part of the migration.