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.
I’m guessing you can’t actually see completely into the machine but are looking past the door into a plastic edge of the case. Laser light won’t go around corners. As far as smoke coming out… Again during operation it should not. Only after the fans stop when most of the smoke is supposed to already be vented. It’s not 100% though which is why some want more control of the fans. Doesn’t bother me or my large studio space.
You can’t seal all of the cracks and if the fans are working correctly should not need to do so. Think of the very large slot in the front and back of the Pro units. It’s a huge gap and was engineered to work that way.
From what I can gather from customer support the lid should be flush, but it will be based on the surface you’re placing it on. All machines are tested on magical granite slabs polished by woodland elves with diamond dust and laser levelers or some such thing.
Mine was pretty level but still wouldn’t close easily, after being told it was tested by woodland creatures I forced it shut a few times and that seemed to help align the lid a bit better and close more or less fully.