I don't use pellets but IMO I do not think that minor crushing of the pellets would be that detrimental to accuracy. And like sabotloader said consistancy is the key to accuracy. As for not seating the bullet on top of the charge, this can be apotentially dangerous situation. Some of the problems that you could see happening is inconsistant accuracy, and anything from a minor barrel bulge to barrel rupture (both of which will severely ruin accuracy, not to mention YOUR day).
This is the main reason why, after loading on a clean barrel, you should put a reference line on your ramrod for sucessive loading depth. I usually use a piece of masking tape as a reference until I find a load my rifle likes, then I put a permanent line on the ramrod.