I think the holes in the side near the bottom will be easier and work just fine.
It seems much simpler than building a new door and moving the hinge location. I suspect both would work equally well as the problem was the air intake was originally way above the pellet tray and either solution will move it to the same plane as the pellet tray. You want the fresh air to flow over the pellets as it gets pulled by the heat convection upwards into the smoke chamber. It might also make for a more even pellet burn if the holes were on the side. If the air is flowing from the front and then can go to the left into the main chamber, it is not as even a flow as it would be from the side where the air is flowing across the tray before entering the main chamber. I don't know that it would really matter, but with the front and that big side opening into the main chamber I could see where the pellets towards the front of the tray would be getting better air flow than the ones in the back. With the holes on the side, the air flow should be even across the entire tray.
Might be splitting hairs though as it obviously works in your test. You might want to let it burn for a number of hours in the test configuration to make sure the air flow from the front does not change the rate of pellet burn as the pellets in the back of the tray are the source of the smoke. I could see where the natural flow of the air from the front opening would be to quickly turn left and head into the main chamber. Might lead to an oxygen starvation situation in the back towards the right of the smoke chamber, but I don't think it will be nearly as bad as when you started.