Notes and Calendar are the only apps that still use custom launch images. I always found it to be more annoying than useful because you can't tell when the damn app has actually started running, so it's no surprise that they didn't make that feature available to third-party apps.

But if you look at Apple's other software, say, iBooks or Remote.app, the launch image often doesn't match the initial UI presented when the app starts running. I don't think it's much of an issue.

In the case of Instapaper, I might consider doing a very fast animation from light to dark, when necessary, but I wouldn't spend much time on it.