Forum members are welcome to comment with their expertise, but here is my answer.
The tiles are hand made which makes them so durable and ensure the high quality, yet they do have very slight default to the eye if put against a straight edge. A few extra tiles are provided just in case there is some damage during the shipping or too great of an imperfection on a tile.
Machine made tiles may appear perfect to the eye but will show their default once exposed to the heat.
1) Yes, it is just fine and I can guaranty you that the result when cooking will be perfect
2) As described in the installation guide you can put a little of the refractory clay,mixed with sand, under the wobbly tiles to level it perfectly. But with something of 1 mm or less, you can just let it as is. Once you start burning the wood, it will settle nicely
3) The tiles need that space to freely expend and retract. Once you will have cured your oven, any of the minor gap you describe will be barely visible.
4) As described in the installation guide you need to fill the gap on the perimeter of the floor where the tiles and the concrete meet with the refractory clay. Do not fill the space with bricks, this space is necessary as well so the tiles can expend and retract (otherwise they will crack over time). Once you place the dome, part of the gap will be covered.
Let me know if you need anything else.