Proper Swiss Emmentaler is made in special forms, usually what is called a Järb, which is a fixed height form with adjustable diameter, or a Vätter, which is a fixed dia. form with follower. Neither of these have holes.
As for increasing the weight at the end to ensure knit, this is a non factor, if it is not thoroughly knit by this time, it is not going to be (at least that's my thought) The knitting should all occur during the first few pressings. The later pressings are to drive out moisture and to get rid of any flaws.
Part of the reason we keep the cheese covered, or in the case of a small cheese press it under whey, is because the temp. is needed for knitting. By the final press, there is not enough warmth left in the cheese to knit it any more.
As for the nubs, they tell me they go away. But if I was making a cheese that got nubs on it, my Swiss obsessiveness would lead me to remove them.
Don't forget to trim those corners either!