This has... not been my experience at all. I mean, maybe it's just that I haven't worked on big enough deals? But my experience is that flexibility exists at the "handshake deal" size, but once the total deal value surpasses, say, the value of a nice used honda civic, professionals are excellent at squeezing as much surplus value (in dollars, of course) from the deal, and negotiation on things that are not money is largely impossible.
Now, for me? this has been true for every large deal. However, every large deal I've done has been with someone staggeringly larger than I am. (the largest was probably a co-lo deal with a staggeringly large co-location provider... with a total deal value above a quarter million bucks, so I'm small fry.)
Players that are my size or smaller are willing to be super flexible about everything, like you describe, but the deal value is usually so small that the only profit to be had is that it's fun to work with them, or that I get to learn something from them. And yeah, that's good and important and stuff, and I do a lot of deals at that level, but I almost think of this more as a social thing; network building and/or drinking with friends. I could do deals at that level all day every day and make rent, but there's no way I'd come close to what I can get as a moderately competent contract linux sysadmin working for a giant faceless company.
Why is this? Well, small companies, generally speaking, just don't have huge amounts of cash to throw around. And large companies? for large companies, I think it has a lot to do with what tptacek said about legal costs. A long time ago, there was talk of selling my company. I mean, it ended up being that they wanted to hire me for two years, at 30% more than I could get as a consultant, plus some performance bonuses that would depend as much on their actions as mine. But the total deal value would have been almost but not quite twice my previous largest deal value. Still, small potatoes, by the standards of such things. They were larger than I was... but still pretty small by industry standards, so they were willing to be super flexible, though they needed to keep the deal size super small.
The point I was making was that legal would have eaten all of the difference between what they wanted to pay for me & the company and what I can get paid as a contractor. The less standard the deal, the more it costs in legal. I imagine this is why large companies are so... inflexible on sub-MM deals. They have standard deals that have been approved by legal, and they don't want to spend the money to get a new deal approved.
So.. yeah, that's my experience. Deals are either handshake deals, with amounts of money changing hands that really don't matter (and I've bought companies at that level; It's common in the hosting industry, when someone is tired of running their company.) or they are large enough that legal is involved, in which case, unless it's a truly staggering amount of money, the giant cost of legal makes the deal way less interesting.
I've seen the same thing in employment. If you wanna work for someone like me for $15/hr, you can get all kinds of flexibility, no problem.
If you want to work for said faceless company and make decent money? you do it their way. You conform to their standard deal. I mean, they have a lot of standard deals you can conform to... and conforming to any of them is just fine, but pick one and quit fucking around.
(I mean, if you are an incredible person, again, it's probably different. But if you are a mortal who maxes out somewhere between $70 and $100/hr like most of us... you conform to their deal structure, or you come work for someone like me at 1/5th that.)