The alignment is not the issue, they are all sound from a real-life football perspective.
The problem is that video game football is not the same as real-life. Each gap is accounted for in the clips you chose, however, the execution is terrible in the 2nd clip and the playside LB is
unblocked in the 3rd, however he doesn't make the play.
As for the shifting in the 2nd play, so what? That's exactly how an over defense would align to the formation. In real football (especially in college and below), many fronts are called to the field or the boundary, making the offensive formation insignificant. They are not out-numbered and the if the corner would've replaced against the crack block properly, the play goes for a loss.
I don't know if I'm seeing things different than you in that 3rd clip, but this is what I am seeing:
....................F............................. .....SS..........................................
.................................................. ...........................................
.C.........................B...........M.......... .................................C................
.......................W....T...N...T.........S... ..............................................
.X......................T...G..C..G...T..Y........ ..........................
.....................................Q............ .................................Z................
...........................................F...... .........................................
.....................................T............ .........................................
That is a standard 2 high look vs a normal 21 personnel formation. In the play, neither ILB is blocked, because the FB goes directly at the SS.
If you want to bring down a safety, fine, but that's a different defense.