That particular situation is an interesting one. Its tough to "gameplan" for that exact situation. In real life, with no timeouts and 13 seconds left.....what do you do? Not enough time for a running play to the center of the field, spike it on 3rd, then kick a FG on 4th down. Maybe throw a pass, but like the OP said...it HAS to be into the endzone....or you risk running out of time, which is what happened.
So that leaves us with the only good option....kick the FG on 2nd down with 13 seconds left.
But....how do you gameplan for that exact situation? I cant'. You might be inside the 20, but you might be on the 19 or you might be on the 1. In real life, that probably makes a difference.
It seems to me that the engine needs a bit of a logic tweak, to allow for a FG in that situation (not enough time to run a play, spike, then kick...so just kick).