But assuming two networks with the same hash rate, a smaller avg. time causes reduced difficulty. This increases variance and counters this effect, no?
Assuming the same number of confirmations, there is the same variance in the number of blocks found by the attacker.
Assuming the same wait time, a reduced difficulty means more blocks found on average. For Poisson-distributed variables, the variance is equal to the mean, so the standard deviation is equal to the square root of the mean. With a larger mean, the relative standard deviation is lower.
It also seems more economical to try an attack on the chain with the lower difficulty, since the expected cost for one attempt is lower, but the expected return is realistically the same.
Yes. But this is dwarfed by the fact that with a lower difficulty, you can increase the number of confirmations with the same wait time and greatly reduce the probability of success (which is the main factor in the economics of the attack).
In the .pdf, things start to look bad for honest side once you asumed attacker pre-mined one block. How can he do that?
The attacker can mine away and only start the attack when he finds a block. This is easy to do even with a low hashrate. If you are familiar with the Finney attack, it is a special case of this where the number of confirmations is 0, and hence the probability of success is 100%, with any hashrate.
And why not pre-mine more than just one block?
He could do that, and a fuller treatment of this is under the scope of the economic discussion. However, there is a big gap in the effectiveness of pre-mining one vs. two. Pre-mining 1 block is a "sure thing" as the attacker counts on finding a block anyway, so he may as well postpone the attack until he does. But after he finds the first block, waiting to get more blocks just puts him at risk that the honest network will regain the lead. If this happens he loses the reward of the block he found. He is in a hashrate disadvantage so he's better off pressing his head start.
If the only attack cost is the lost block reward, then he should pre-mine just one block because the risk of losing the reward is the same and this gives him a better chance to benefit from it. If, however, the main cost is the illiquidity of the goods purchased, he should indeed make multiple attempts to pre-mine several blocks, and call the thing off with every failure.