I tried downloading the APK but I didn't want to install their app or plugin.
But my educated guess of what you are experiencing (because I've
fought with this before in other contexts (i.e. not SDL)), is that the
fact that SDL's Android implementation runs on a background thread is
the source of your problem, and why you don't have the problem with
your native comparison program.
Because SDL is not running on the main UI thread, as your real Android
input events happen, they are being queued up to be handled by the SDL
event later when the OS switches back to the SDL thread. This
unfortunately interferes with perfect responsiveness.
However, I expected behavior more like Eric Wasylishen's description
of a lag, and not a micro stutter.