Agree on the seal possibly being a problem. If it is, they would have had to have moved the striker post out as well, as it tightly controls the position of the door when closed. If they didn't move the striker post out, you simply would not be able to get the door to completely latch.
Having recently replaced the seals on another (non-Fiat) vehicle I own, I had the same problem - I had to adjust the striker plate outwards, and it took a REALLY hard slam to get the door to latch all the way. Everyone on the vehicle forum said that the seal will relax over time, it's been several months and it really hasn't relaxed much at all.
One other thing that was pointed out is that the seal is kind of a big balloon. In the case of this seal, it ran continually around the door, and then plugged back into itself with a tube. When the door is slammed, there is no where for the air to go, and it compresses and springs back against the door, making it much harder to close. It was then pointed out that the factory seals (Ford, in this case) had holes it in every foot or so, to allow the air to escape and lessen the spring-back effect. The aftermarket seals I installed did not have that. I experimented with carefully poking a few holes with an Xacto razor, it seemed to help a bit. I don't know if the X1/9 door seal is a continuous balloon, or if it has open ends for the air to escape.