The problem is that deals are usually to lessen the steep payout structure. I've yet to get far enough in a big tournament to get to make deals, but I'm pretty sure it's basically they try to keep similar ev but less difference between the payouts. For example say it's HU deep in a big tourney, 5k for 2nd and 13k for 1st. Say they're around even in chips, they could say "we're both going to get 5k so now we're playing an 8k HU tourney. Let's just give each of us 3.5k and play for 1k.
So then 1st would get 9.5k and 2nd would get 8.5k. ev is still the same
Say 1st instead has a 2:1 chip lead. In that case you say "we each have 5k, now for the remaining 8k take 7, 1st gets 4.67k and 2nd gets 2.33k of that, and we play for the last 1k.
At least that's how I'd format deals if I were in charge of one I was in. I'm not sure how others are proposed, but the overall point is to lessen the variance I'm pretty sure, because although like in cash games people are playing many many hands and smaller tournaments people play again and again, that one situation may never come up again in a player's life even. Basically the logic is I would flip a 60-40 coin 10,000 times for my life's savings, where each flip represents playing for a 10,000th of my life's savings but I would not flip once with that coin for my life's savings. Same exact ev, totally different expected result. If I'll see the situation 10,000 more times I'm fine taking it as it is, but when it's a once in a lifetime chance, some people prefer the security over gambling big.