I wouldn't sweat about the low soil. As long as its not to compact the plants should grow great. A little soil compaction is expected with the first watering. Also, if you find that the soil level is to low then you can always add new soil to the pot after the seedling is established.
Piling soil up on the stem of a seedling, or transplanting a seedling as deep as its cotyledons (its seed leaves) is not uncommon. As long as the seedling is far enough along to withstand stem rot at the soil's surface, the plant will develope roots along the buried stem.
You are right to err on the side of caution with watering. It is so easy to overwater seedlings. Most people are so over attentive to their seeds that they overwater/mist way to much. I know I use to to be guilty of this error myself, but MJ roots like to get nice and dry before they get another drink.
You sound like you know your shit. I am sure your first grow and journal will have killer results. Keep us posted.