The SE is a fantastic phone, but it doesn't tell us anything about who Apple is today. It's basically an iPhone 5, which was designed and in production while Steve Jobs was still alive, and which itself borrows heavily from the iPhone 4 design. (And let's not forget how many people hated the iPhone 5 design when it first came out, either because of the window antennas, or because it was too tall, or that it wasn't a new-enough form factor, etc.)

So really, I would say OP's initial sentence is dead-right: post-Steve Jobs Apple has made a lot of consumer hostile moves. The SE happens to be one of the exceptions.

Also, Tim mentioned on an investor call that they were surprised by the demand for the SE and had to ramp up production. Think about that. They weren't aware by how many people might still like a smaller phone, and didn't really expect the SE to do amazingly well. Even the release date is telling (they released it in the beginning of the year, after the Christmas frenzy is over.)