No worries. The lid center glass and side glass is not flush on any of the machines. However the front top left and top right lid corners should be reasonably flush with the sides. If not, your unit may not be sitting perfectly flat. Shimming the corners under the unit’s foot runners will usually make the lid fit a little better and flush at the top front corners.
If smoke is entering the room during operation the culprit is almost always a bad vent seal or other obstruction with the venting arrangement. Many of us are using metal foil tape to better seal the connection at the machine and other end of the vent hose. The fans create a negative pressure inside the unit during operation. Even very large cracks, including the Pro pass thru will not normally leak smoke. After the fans shut down residual smell/smoke (hopefully very little) will often enter the room.