Hmm, it is, just not my first choice if a seal is available.
The seal gets installed in the cutout in the body. Then, from the outside of the vehicle, with inner wheel well removed and out of the way, the evaporator housing is slid in to an opening in the front of the passenger side cowl. The seals puts pressure against the evaporator housing, but also overlaps the cutout in the body so that water running down inside the cowl can’t enter the car.
To use putty or a pliable sealer, I’m afraid that when the bond between the sealer and the body breaks down, then water will come right in again.